data_35011 ####################### # Entry information # ####################### save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID 35011 _Entry.Title ; A tetrameric i-motif structure formed by dTdCdCfrCdCdC ; _Entry.Type macromolecule _Entry.Version_type original _Entry.Submission_date 2025-08-01 _Entry.Accession_date 2025-08-01 _Entry.Last_release_date 2025-10-06 _Entry.Original_release_date 2025-10-06 _Entry.Origination author _Entry.Format_name . _Entry.NMR_STAR_version 3.2.14.0 _Entry.NMR_STAR_dict_location . _Entry.Original_NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype 'SOLUTION NMR' _Entry.Source_data_format . _Entry.Source_data_format_version . _Entry.Generated_software_name . _Entry.Generated_software_version . _Entry.Generated_software_ID . _Entry.Generated_software_label . _Entry.Generated_date . _Entry.DOI . _Entry.UUID . _Entry.Related_coordinate_file_name . _Entry.Details . _Entry.BMRB_internal_directory_name . loop_ _Entry_author.Ordinal _Entry_author.Given_name _Entry_author.Family_name _Entry_author.First_initial _Entry_author.Middle_initials _Entry_author.Family_title _Entry_author.ORCID _Entry_author.Entry_ID 1 C. Ugedo C. . . . 35011 2 A. Dominguez A. . . . 35011 3 I. Gomez-Pinto I. . . . 35011 4 R. Eritja R. . . . 35011 5 A. Avino A. . . . 35011 6 C. Gonzalez C. . . . 35011 stop_ loop_ _Struct_keywords.Keywords _Struct_keywords.Text _Struct_keywords.Entry_ID 'DNA-RNA HYBRID' . 35011 XNA . 35011 'fluorine substitution' . 35011 i-motif . 35011 stop_ loop_ _Data_set.Type _Data_set.Count _Data_set.Entry_ID assigned_chemical_shifts 1 35011 stop_ loop_ _Datum.Type _Datum.Count _Datum.Entry_ID '19F chemical shifts' 1 35011 '1H chemical shifts' 58 35011 stop_ loop_ _Release.Release_number _Release.Format_type _Release.Format_version _Release.Date _Release.Submission_date _Release.Type _Release.Author _Release.Detail _Release.Entry_ID 1 . . 2025-10-08 . original BMRB . 35011 stop_ loop_ _Related_entries.Database_name _Related_entries.Database_accession_code _Related_entries.Relationship _Related_entries.Entry_ID PDB 9S6Z 'BMRB Entry Tracking System' 35011 stop_ save_ ############### # Citations # ############### save_citation_1 _Citation.Sf_category citations _Citation.Sf_framecode citation_1 _Citation.Entry_ID 35011 _Citation.ID 1 _Citation.Name . _Citation.Class 'entry citation' _Citation.CAS_abstract_code . _Citation.MEDLINE_UI_code . _Citation.PubMed_ID 40942089 _Citation.DOI 10.3390/molecules30173561 _Citation.Full_citation . _Citation.Title ; The Effect of 2'F-RNA on I-Motif Structure and Stability. ; _Citation.Status published _Citation.Type journal _Citation.Journal_abbrev Molecules _Citation.Journal_name_full . _Citation.Journal_volume 30 _Citation.Journal_issue . _Citation.Journal_ASTM . _Citation.Journal_ISSN 1420-3049 _Citation.Journal_CSD . _Citation.Book_title . _Citation.Book_chapter_title . _Citation.Book_volume . _Citation.Book_series . _Citation.Book_publisher . _Citation.Book_publisher_city . _Citation.Book_ISBN . _Citation.Conference_title . _Citation.Conference_site . _Citation.Conference_state_province . _Citation.Conference_country . _Citation.Conference_start_date . _Citation.Conference_end_date . _Citation.Conference_abstract_number . _Citation.Thesis_institution . _Citation.Thesis_institution_city . _Citation.Thesis_institution_country . _Citation.WWW_URL . _Citation.Page_first . _Citation.Page_last . _Citation.Year 2025 _Citation.Details . loop_ _Citation_author.Ordinal _Citation_author.Given_name _Citation_author.Family_name _Citation_author.First_initial _Citation_author.Middle_initials _Citation_author.Family_title _Citation_author.ORCID _Citation_author.Entry_ID _Citation_author.Citation_ID 1 C. Ugedo C. . . . 35011 1 2 A. Dominguez A. . . . 35011 1 3 I. Gomez-Pinto I. . . . 35011 1 4 R. Eritja R. . . . 35011 1 5 C. Gonzalez C. . . . 35011 1 6 A. Avino A. . . . 35011 1 stop_ save_ ############################################# # Molecular system (assembly) description # ############################################# save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID 35011 _Assembly.ID 1 _Assembly.Name "DNA (5'-D(*TP*CP*CP*(CFZ)P*(DNR)P*C)-3'), DNA (5'-D(*TP*(DNR)P*(DNR)P*(CFZ)P*CP*(DNR))-3')" _Assembly.BMRB_code . _Assembly.Number_of_components . _Assembly.Organic_ligands . _Assembly.Metal_ions . _Assembly.Non_standard_bonds . _Assembly.Ambiguous_conformational_states . _Assembly.Ambiguous_chem_comp_sites . _Assembly.Molecules_in_chemical_exchange . _Assembly.Paramagnetic no _Assembly.Thiol_state . _Assembly.Molecular_mass . _Assembly.Enzyme_commission_number . _Assembly.Details . _Assembly.DB_query_date . _Assembly.DB_query_revised_last_date . loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 unit_1 1 $entity_1 A A no . . . . . . 35011 1 2 unit_2 1 $entity_1 B B no . . . . . . 35011 1 3 unit_3 2 $entity_2 C C yes . . . . . . 35011 1 4 unit_4 2 $entity_2 D D yes . . . . . . 35011 1 stop_ save_ #################################### # Biological polymers and ligands # #################################### save_entity_1 _Entity.Sf_category entity _Entity.Sf_framecode entity_1 _Entity.Entry_ID 35011 _Entity.ID 1 _Entity.BMRB_code . _Entity.Name entity_1 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID A,B _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; TCCXXC ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states . _Entity.Ambiguous_chem_comp_sites . _Entity.Nstd_monomer yes _Entity.Nstd_chirality . _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 6 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method syn _Entity.Parent_entity_ID 1 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight 1724.143 _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details 'Structure of an homotetrameric i-motif. All cytosine pairs hemiprotonated.' _Entity.DB_query_date . _Entity.DB_query_revised_last_date . loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . DT . 35011 1 2 . DC . 35011 1 3 . DC . 35011 1 4 . CFZ . 35011 1 5 . DNR . 35011 1 6 . DC . 35011 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . DT 1 1 35011 1 . DC 2 2 35011 1 . DC 3 3 35011 1 . CFZ 4 4 35011 1 . DNR 5 5 35011 1 . DC 6 6 35011 1 stop_ save_ save_entity_2 _Entity.Sf_category entity _Entity.Sf_framecode entity_2 _Entity.Entry_ID 35011 _Entity.ID 2 _Entity.BMRB_code . _Entity.Name entity_2 _Entity.Type polymer _Entity.Polymer_common_type . _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_type_details . _Entity.Polymer_strand_ID C,D _Entity.Polymer_seq_one_letter_code_can . _Entity.Polymer_seq_one_letter_code ; TXXXCX ; _Entity.Target_identifier . _Entity.Polymer_author_defined_seq . _Entity.Polymer_author_seq_details . _Entity.Ambiguous_conformational_states . _Entity.Ambiguous_chem_comp_sites . _Entity.Nstd_monomer yes _Entity.Nstd_chirality . _Entity.Nstd_linkage no _Entity.Nonpolymer_comp_ID . _Entity.Nonpolymer_comp_label . _Entity.Number_of_monomers 6 _Entity.Number_of_nonpolymer_components . _Entity.Paramagnetic no _Entity.Thiol_state 'not present' _Entity.Src_method syn _Entity.Parent_entity_ID 2 _Entity.Fragment . _Entity.Mutation . _Entity.EC_number . _Entity.Calc_isoelectric_point . _Entity.Formula_weight 1726.159 _Entity.Formula_weight_exptl . _Entity.Formula_weight_exptl_meth . _Entity.Details 'Structure of an homotetrameric i-motif. All cytosine pairs hemiprotonated.' _Entity.DB_query_date . _Entity.DB_query_revised_last_date . loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . DT . 35011 2 2 . DNR . 35011 2 3 . DNR . 35011 2 4 . CFZ . 35011 2 5 . DC . 35011 2 6 . DNR . 35011 2 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . DT 1 1 35011 2 . DNR 2 2 35011 2 . DNR 3 3 35011 2 . CFZ 4 4 35011 2 . DC 5 5 35011 2 . DNR 6 6 35011 2 stop_ save_ #################### # Natural source # #################### save_natural_source _Entity_natural_src_list.Sf_category natural_source _Entity_natural_src_list.Sf_framecode natural_source _Entity_natural_src_list.Entry_ID 35011 _Entity_natural_src_list.ID 1 loop_ _Entity_natural_src.ID _Entity_natural_src.Entity_ID _Entity_natural_src.Entity_label _Entity_natural_src.Entity_chimera_segment_ID _Entity_natural_src.NCBI_taxonomy_ID _Entity_natural_src.Type _Entity_natural_src.Common _Entity_natural_src.Organism_name_scientific _Entity_natural_src.Organism_name_common _Entity_natural_src.Organism_acronym _Entity_natural_src.ICTVdb_decimal_code _Entity_natural_src.Superkingdom _Entity_natural_src.Kingdom _Entity_natural_src.Genus _Entity_natural_src.Species _Entity_natural_src.Strain _Entity_natural_src.Variant _Entity_natural_src.Organ _Entity_natural_src.Tissue _Entity_natural_src.Tissue_fraction _Entity_natural_src.Cell_line _Entity_natural_src.Cell_type _Entity_natural_src.ATCC_number _Entity_natural_src.Organelle _Entity_natural_src.Secretion _Entity_natural_src.Plasmid _Entity_natural_src.Gene_mnemonic _Entity_natural_src.Details _Entity_natural_src.Entry_ID _Entity_natural_src.Entity_natural_src_list_ID 1 1 $entity_1 . 32630 'no natural source' . 'synthetic construct' . . . . . synthetic construct . . . . . . . . . . . . . 35011 1 2 2 $entity_2 . 32630 'no natural source' . 'synthetic construct' . . . . . synthetic construct . . . . . . . . . . . . . 35011 1 stop_ save_ ######################### # Experimental source # ######################### save_experimental_source _Entity_experimental_src_list.Sf_category experimental_source _Entity_experimental_src_list.Sf_framecode experimental_source _Entity_experimental_src_list.Entry_ID 35011 _Entity_experimental_src_list.ID 1 loop_ _Entity_experimental_src.ID _Entity_experimental_src.Entity_ID _Entity_experimental_src.Entity_label _Entity_experimental_src.Entity_chimera_segment_ID _Entity_experimental_src.Production_method _Entity_experimental_src.Host_org_scientific_name _Entity_experimental_src.Host_org_name_common _Entity_experimental_src.Host_org_details _Entity_experimental_src.Host_org_NCBI_taxonomy_ID _Entity_experimental_src.Host_org_genus _Entity_experimental_src.Host_org_species _Entity_experimental_src.Host_org_strain _Entity_experimental_src.Host_org_variant _Entity_experimental_src.Host_org_ATCC_number _Entity_experimental_src.Vector_type _Entity_experimental_src.PDBview_host_org_vector_name _Entity_experimental_src.PDBview_plasmid_name _Entity_experimental_src.Vector_name _Entity_experimental_src.Vector_details _Entity_experimental_src.Vendor_name _Entity_experimental_src.Details _Entity_experimental_src.Entry_ID _Entity_experimental_src.Entity_experimental_src_list_ID 1 1 $entity_1 . 'chemical synthesis' . . . . . . . . . . . . . . . . 35011 1 2 2 $entity_2 . 'chemical synthesis' . . . . . . . . . . . . . . . . 35011 1 stop_ save_ ################################# # Polymer residues and ligands # ################################# save_chem_comp_CFZ _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_CFZ _Chem_comp.Entry_ID 35011 _Chem_comp.ID CFZ _Chem_comp.Provenance PDB _Chem_comp.Name "2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)" _Chem_comp.Type 'DNA LINKING' _Chem_comp.BMRB_code CFZ _Chem_comp.PDB_code CFZ _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2020-07-10 _Chem_comp.Modified_date 2020-07-10 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code . _Chem_comp.Three_letter_code CFZ _Chem_comp.Number_atoms_all 34 _Chem_comp.Number_atoms_nh 21 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code ; InChI=1S/C9H13FN3O7P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)13-2-1-5(11)12-9(13)15/h1-2,4,6-8,14H,3H2,(H2,11,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 ; _Chem_comp.Mon_nstd_flag no _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID DC _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms . _Chem_comp.Formal_charge 0 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C9 H13 F N3 O7 P' _Chem_comp.Formula_weight 325.188 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag no _Chem_comp.Ideal_coordinates_details Corina _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code 3AGV _Chem_comp.Processing_site PDBJ _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)F SMILES 'OpenEye OEToolkits' 1.7.0 35011 CFZ C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)F SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.0 35011 CFZ ; InChI=1S/C9H13FN3O7P/c10-6-7(14)4(3-19-21(16,17)18)20-8(6)13-2-1-5(11)12-9(13)15/h1-2,4,6-8,14H,3H2,(H2,11,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1 ; InChI InChI 1.03 35011 CFZ KTAATIGPZHTGOP-XVFCMESISA-N InChIKey InChI 1.03 35011 CFZ NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2F SMILES_CANONICAL CACTVS 3.370 35011 CFZ NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2F SMILES CACTVS 3.370 35011 CFZ O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(F)C2O SMILES ACDLabs 12.01 35011 CFZ stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID "2'-deoxy-2'-fluorocytidine 5'-(dihydrogen phosphate)" 'SYSTEMATIC NAME' ACDLabs 12.01 35011 CFZ '[(2R,3R,4R,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.0 35011 CFZ stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID P P P P . P . . N 0 . . . 1 N N . . . . 33.646 . 15.023 . 24.064 . 4.176 1.031 0.067 1 . 35011 CFZ N1 N1 N1 N1 . N . . N 0 . . . 1 N N . . . . 33.918 . 9.728 . 23.714 . -2.467 0.031 0.464 2 . 35011 CFZ C2 C2 C2 C2 . C . . N 0 . . . 1 N N . . . . 33.873 . 8.458 . 23.133 . -2.544 0.708 -0.696 3 . 35011 CFZ O2 O2 O2 O2 . O . . N 0 . . . 1 N N . . . . 34.456 . 7.519 . 23.695 . -1.667 0.569 -1.532 4 . 35011 CFZ N3 N3 N3 N3 . N . . N 0 . . . 1 N N . . . . 33.199 . 8.285 . 21.974 . -3.563 1.528 -0.946 5 . 35011 CFZ C4 C4 C4 C4 . C . . N 0 . . . 1 N N . . . . 32.595 . 9.322 . 21.393 . -4.530 1.699 -0.054 6 . 35011 CFZ N4 N4 N4 N4 . N . . N 0 . . . 1 N N . . . . 31.932 . 9.101 . 20.256 . -5.578 2.548 -0.324 7 . 35011 CFZ C5 C5 C5 C5 . C . . N 0 . . . 1 N N . . . . 32.641 . 10.632 . 21.953 . -4.478 1.004 1.171 8 . 35011 CFZ C6 C6 C6 C6 . C . . N 0 . . . 1 N N . . . . 33.308 . 10.788 . 23.104 . -3.439 0.169 1.408 9 . 35011 CFZ C1' C1' C1' C1' . C . . R 0 . . . 1 N N . . . . 34.623 . 9.896 . 24.995 . -1.334 -0.865 0.710 10 . 35011 CFZ O1P O1P O1P O1P . O . . N 0 . . . 1 N N . . . . 34.400 . 16.152 . 24.668 . 4.620 2.004 1.270 11 . 35011 CFZ C2' C2' C2' C2' . C . . R 0 . . . 1 N N . . . . 36.139 . 9.933 . 24.848 . -1.311 -2.003 -0.334 12 . 35011 CFZ F2' F2' F2' F2' . F . . N 0 . . . 1 N N . . . . 36.798 . 9.427 . 25.992 . -1.886 -3.164 0.194 13 . 35011 CFZ O2P O2P O2P O2P . O . . N 0 . . . 1 N N . . . . 33.272 . 15.065 . 22.626 . 3.925 1.834 -1.150 14 . 35011 CFZ C3' C3' C3' C3' . C . . R 0 . . . 1 N N . . . . 36.390 . 11.427 . 24.671 . 0.192 -2.224 -0.616 15 . 35011 CFZ O3' O3' O3' O3' . O . . N 0 . . . 1 N N . . . . 37.746 . 11.809 . 24.905 . 0.579 -3.553 -0.259 16 . 35011 CFZ O3P O3P O3P O3P . O . . N 0 . . . 1 N Y . . . . 32.311 . 14.855 . 24.934 . 5.349 -0.033 -0.224 17 . 35011 CFZ C4' C4' C4' C4' . C . . R 0 . . . 1 N N . . . . 35.439 . 11.985 . 25.716 . 0.900 -1.193 0.291 18 . 35011 CFZ O4' O4' O4' O4' . O . . N 0 . . . 1 N N . . . . 34.254 . 11.152 . 25.557 . -0.086 -0.162 0.517 19 . 35011 CFZ C5' C5' C5' C5' . C . . N 0 . . . 1 N N . . . . 35.045 . 13.434 . 25.589 . 2.126 -0.614 -0.417 20 . 35011 CFZ O5' O5' O5' O5' . O . . N 0 . . . 1 N N . . . . 34.447 . 13.674 . 24.328 . 2.831 0.248 0.479 21 . 35011 CFZ HN4 HN4 HN4 HN4 . H . . N 0 . . . 1 N N . . . . 31.900 . 8.180 . 19.867 . -5.612 3.025 -1.168 22 . 35011 CFZ HN4A HN4A HN4A HN4A . H . . N 0 . . . 0 N N . . . . 31.467 . 9.856 . 19.793 . -6.284 2.671 0.330 23 . 35011 CFZ H5 H5 H5 H5 . H . . N 0 . . . 1 N N . . . . 32.157 . 11.467 . 21.468 . -5.258 1.132 1.908 24 . 35011 CFZ H6 H6 H6 H6 . H . . N 0 . . . 1 N N . . . . 33.365 . 11.767 . 23.557 . -3.377 -0.375 2.339 25 . 35011 CFZ H1' H1' H1' H1' . H . . N 0 . . . 1 N N . . . . 34.343 . 9.034 . 25.618 . -1.387 -1.274 1.719 26 . 35011 CFZ HO1P HO1P HO1P HO1P . H . . N 0 . . . 0 N N . . . . 34.563 . 16.814 . 24.007 . 5.425 2.509 1.091 27 . 35011 CFZ H2' H2' H2' H2' . H . . N 0 . . . 1 N N . . . . 36.519 . 9.310 . 24.025 . -1.831 -1.699 -1.242 28 . 35011 CFZ H3' H3' H3' H3' . H . . N 0 . . . 1 N N . . . . 36.222 . 11.792 . 23.647 . 0.417 -2.030 -1.665 29 . 35011 CFZ HO3' HO3' HO3' HO3' . H . . N 0 . . . 0 N Y . . . . 37.838 . 12.746 . 24.780 . 0.119 -4.243 -0.757 30 . 35011 CFZ HO3P HO3P HO3P HO3P . H . . N 0 . . . 0 N Y . . . . 31.558 . 14.817 . 24.356 . 5.566 -0.595 0.533 31 . 35011 CFZ H4' H4' H4' H4' . H . . N 0 . . . 1 N N . . . . 35.938 . 11.960 . 26.696 . 1.190 -1.654 1.235 32 . 35011 CFZ H5' H5' H5' H5' . H . . N 0 . . . 1 N N . . . . 34.326 . 13.684 . 26.383 . 2.782 -1.426 -0.731 33 . 35011 CFZ H5'A H5'A H5'A H5'A . H . . N 0 . . . 0 N N . . . . 35.942 . 14.062 . 25.689 . 1.807 -0.046 -1.291 34 . 35011 CFZ stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . DOUB O2P P N N 1 . 35011 CFZ 2 . SING P O5' N N 2 . 35011 CFZ 3 . SING P O1P N N 3 . 35011 CFZ 4 . SING P O3P N N 4 . 35011 CFZ 5 . SING C6 N1 N N 5 . 35011 CFZ 6 . SING C2 N1 N N 6 . 35011 CFZ 7 . SING N1 C1' N N 7 . 35011 CFZ 8 . SING N3 C2 N N 8 . 35011 CFZ 9 . DOUB C2 O2 N N 9 . 35011 CFZ 10 . DOUB C4 N3 N N 10 . 35011 CFZ 11 . SING N4 C4 N N 11 . 35011 CFZ 12 . SING C4 C5 N N 12 . 35011 CFZ 13 . SING N4 HN4 N N 13 . 35011 CFZ 14 . SING N4 HN4A N N 14 . 35011 CFZ 15 . DOUB C5 C6 N N 15 . 35011 CFZ 16 . SING C5 H5 N N 16 . 35011 CFZ 17 . SING C6 H6 N N 17 . 35011 CFZ 18 . SING C2' C1' N N 18 . 35011 CFZ 19 . SING C1' O4' N N 19 . 35011 CFZ 20 . SING C1' H1' N N 20 . 35011 CFZ 21 . SING O1P HO1P N N 21 . 35011 CFZ 22 . SING C3' C2' N N 22 . 35011 CFZ 23 . SING C2' F2' N N 23 . 35011 CFZ 24 . SING C2' H2' N N 24 . 35011 CFZ 25 . SING C3' O3' N N 25 . 35011 CFZ 26 . SING C3' C4' N N 26 . 35011 CFZ 27 . SING C3' H3' N N 27 . 35011 CFZ 28 . SING O3' HO3' N N 28 . 35011 CFZ 29 . SING O3P HO3P N N 29 . 35011 CFZ 30 . SING O4' C4' N N 30 . 35011 CFZ 31 . SING C5' C4' N N 31 . 35011 CFZ 32 . SING C4' H4' N N 32 . 35011 CFZ 33 . SING O5' C5' N N 33 . 35011 CFZ 34 . SING C5' H5' N N 34 . 35011 CFZ 35 . SING C5' H5'A N N 35 . 35011 CFZ stop_ save_ save_chem_comp_DNR _Chem_comp.Sf_category chem_comp _Chem_comp.Sf_framecode chem_comp_DNR _Chem_comp.Entry_ID 35011 _Chem_comp.ID DNR _Chem_comp.Provenance PDB _Chem_comp.Name "2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE" _Chem_comp.Type 'DNA LINKING' _Chem_comp.BMRB_code DNR _Chem_comp.PDB_code DNR _Chem_comp.Ambiguous_flag no _Chem_comp.Initial_date 2020-07-10 _Chem_comp.Modified_date 2020-07-10 _Chem_comp.Release_status REL _Chem_comp.Replaced_by . _Chem_comp.Replaces . _Chem_comp.One_letter_code C _Chem_comp.Three_letter_code DNR _Chem_comp.Number_atoms_all 35 _Chem_comp.Number_atoms_nh 20 _Chem_comp.Atom_nomenclature_source . _Chem_comp.PubChem_code . _Chem_comp.Subcomponent_list . _Chem_comp.InChI_code ; InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/p+1/t5-,6+,8+/m0/s1 ; _Chem_comp.Mon_nstd_flag no _Chem_comp.Mon_nstd_class . _Chem_comp.Mon_nstd_details . _Chem_comp.Mon_nstd_parent . _Chem_comp.Mon_nstd_parent_comp_ID DC _Chem_comp.Std_deriv_one_letter_code . _Chem_comp.Std_deriv_three_letter_code . _Chem_comp.Std_deriv_BMRB_code . _Chem_comp.Std_deriv_PDB_code . _Chem_comp.Std_deriv_chem_comp_name . _Chem_comp.Synonyms . _Chem_comp.Formal_charge 1 _Chem_comp.Paramagnetic . _Chem_comp.Aromatic no _Chem_comp.Formula 'C9 H15 N3 O7 P' _Chem_comp.Formula_weight 308.205 _Chem_comp.Formula_mono_iso_wt_nat . _Chem_comp.Formula_mono_iso_wt_13C . _Chem_comp.Formula_mono_iso_wt_15N . _Chem_comp.Formula_mono_iso_wt_13C_15N . _Chem_comp.Image_file_name . _Chem_comp.Image_file_format . _Chem_comp.Topo_file_name . _Chem_comp.Topo_file_format . _Chem_comp.Struct_file_name . _Chem_comp.Struct_file_format . _Chem_comp.Stereochem_param_file_name . _Chem_comp.Stereochem_param_file_format . _Chem_comp.Model_details . _Chem_comp.Model_erf . _Chem_comp.Model_source . _Chem_comp.Model_coordinates_details . _Chem_comp.Model_coordinates_missing_flag yes _Chem_comp.Ideal_coordinates_details . _Chem_comp.Ideal_coordinates_missing_flag no _Chem_comp.Model_coordinates_db_code 1LAQ _Chem_comp.Processing_site RCSB _Chem_comp.Vendor . _Chem_comp.Vendor_product_code . _Chem_comp.Details . _Chem_comp.DB_query_date . _Chem_comp.DB_last_query_revised_last_date . loop_ _Chem_comp_descriptor.Descriptor _Chem_comp_descriptor.Type _Chem_comp_descriptor.Program _Chem_comp_descriptor.Program_version _Chem_comp_descriptor.Entry_ID _Chem_comp_descriptor.Comp_ID C1C(C(OC1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O SMILES 'OpenEye OEToolkits' 1.5.0 35011 DNR C1[C@@H]([C@H](O[C@H]1N2C=CC(=[NH+]C2=O)N)COP(=O)(O)O)O SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 35011 DNR ; InChI=1S/C9H14N3O7P/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(19-8)4-18-20(15,16)17/h1-2,5-6,8,13H,3-4H2,(H2,10,11,14)(H2,15,16,17)/p+1/t5-,6+,8+/m0/s1 ; InChI InChI 1.03 35011 DNR NC1=[NH+]C(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2 SMILES_CANONICAL CACTVS 3.341 35011 DNR NC1=[NH+]C(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2 SMILES CACTVS 3.341 35011 DNR NCMVOABPESMRCP-SHYZEUOFSA-O InChIKey InChI 1.03 35011 DNR O=C1[NH+]=C(N)C=CN1C2OC(C(O)C2)COP(=O)(O)O SMILES ACDLabs 10.04 35011 DNR stop_ loop_ _Chem_comp_identifier.Identifier _Chem_comp_identifier.Type _Chem_comp_identifier.Program _Chem_comp_identifier.Program_version _Chem_comp_identifier.Entry_ID _Chem_comp_identifier.Comp_ID "2'-deoxy-5'-cytidylic acid" 'SYSTEMATIC NAME' ACDLabs 10.04 35011 DNR '[(2R,3S,5R)-5-(4-amino-2-oxo-pyrimidin-3-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate' 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 35011 DNR stop_ loop_ _Chem_comp_atom.Atom_ID _Chem_comp_atom.BMRB_code _Chem_comp_atom.PDB_atom_ID _Chem_comp_atom.Alt_atom_ID _Chem_comp_atom.Auth_atom_ID _Chem_comp_atom.Type_symbol _Chem_comp_atom.Isotope_number _Chem_comp_atom.Chirality _Chem_comp_atom.Stereo_config _Chem_comp_atom.Charge _Chem_comp_atom.Partial_charge _Chem_comp_atom.Oxidation_number _Chem_comp_atom.Unpaired_electron_number _Chem_comp_atom.Align _Chem_comp_atom.Aromatic_flag _Chem_comp_atom.Leaving_atom_flag _Chem_comp_atom.Substruct_code _Chem_comp_atom.Ionizable _Chem_comp_atom.Drawing_2D_coord_x _Chem_comp_atom.Drawing_2D_coord_y _Chem_comp_atom.Model_Cartn_x _Chem_comp_atom.Model_Cartn_x_esd _Chem_comp_atom.Model_Cartn_y _Chem_comp_atom.Model_Cartn_y_esd _Chem_comp_atom.Model_Cartn_z _Chem_comp_atom.Model_Cartn_z_esd _Chem_comp_atom.Model_Cartn_x_ideal _Chem_comp_atom.Model_Cartn_y_ideal _Chem_comp_atom.Model_Cartn_z_ideal _Chem_comp_atom.PDBX_ordinal _Chem_comp_atom.Details _Chem_comp_atom.Entry_ID _Chem_comp_atom.Comp_ID P P P P . P . . N 0 . . . 1 N N . . . . -0.684 . -7.446 . 15.813 . -3.968 -1.665 3.118 1 . 35011 DNR OP1 OP1 OP1 O1P . O . . N 0 . . . 1 N N . . . . 0.421 . -7.036 . 14.917 . -4.406 -2.599 4.208 2 . 35011 DNR OP2 OP2 OP2 O2P . O . . N 0 . . . 1 N N . . . . -1.407 . -8.711 . 15.556 . -3.912 -2.311 1.636 3 . 35011 DNR O5' O5' O5' O5* . O . . N 0 . . . 1 N N . . . . -1.767 . -6.248 . 15.855 . -2.493 -1.028 3.315 4 . 35011 DNR C5' C5' C5' C5* . C . . N 0 . . . 1 N N . . . . -2.936 . -6.352 . 16.678 . -2.005 -0.136 2.327 5 . 35011 DNR C4' C4' C4' C4* . C . . R 0 . . . 1 N N . . . . -3.852 . -5.142 . 16.542 . -0.611 0.328 2.728 6 . 35011 DNR O4' O4' O4' O4* . O . . N 0 . . . 1 N N . . . . -3.125 . -3.913 . 16.795 . 0.247 -0.829 2.764 7 . 35011 DNR C1' C1' C1' C1* . C . . R 0 . . . 1 N N . . . . -3.181 . -3.066 . 15.625 . 1.157 -0.778 1.657 8 . 35011 DNR N1 N1 N1 N1 . N . . N 0 . . . 1 N N . . . . -1.853 . -2.469 . 15.339 . 1.164 -2.047 0.989 9 . 35011 DNR C6 C6 C6 C6 . C . . N 0 . . . 1 N N . . . . -0.754 . -3.262 . 15.217 . -0.015 -2.783 0.959 10 . 35011 DNR C2 C2 C2 C2 . C . . N 0 . . . 1 N N . . . . -1.760 . -1.079 . 15.249 . 2.335 -2.532 0.381 11 . 35011 DNR O2 O2 O2 O2 . O . . N 0 . . . 1 N N . . . . -2.767 . -0.382 . 15.363 . 3.425 -1.977 0.342 12 . 35011 DNR N3 N3 N3 N3 . N . . N 1 . . . 1 N N . . . . -0.527 . -0.524 . 15.041 . 2.203 -3.824 -0.257 13 . 35011 DNR C4 C4 C4 C4 . C . . N 0 . . . 1 N N . . . . 0.561 . -1.305 . 14.927 . 1.089 -4.548 -0.301 14 . 35011 DNR N4 N4 N4 N4 . N . . N 0 . . . 1 N N . . . . 1.753 . -0.747 . 14.733 . 0.968 -5.729 -0.886 15 . 35011 DNR C5 C5 C5 C5 . C . . N 0 . . . 1 N N . . . . 0.463 . -2.728 . 15.014 . -0.107 -3.974 0.362 16 . 35011 DNR C2' C2' C2' C2* . C . . N 0 . . . 1 N N . . . . -3.671 . -3.939 . 14.490 . 0.710 0.360 0.754 17 . 35011 DNR C3' C3' C3' C3* . C . . S 0 . . . 1 N N . . . . -4.447 . -5.040 . 15.147 . 0.008 1.286 1.720 18 . 35011 DNR O3' O3' O3' O3* . O . . N 0 . . . 1 N N . . . . -5.846 . -4.728 . 15.206 . 0.965 2.121 2.368 19 . 35011 DNR OP3 OP3 OP3 O3P . O . . N 0 . . . 1 N Y . . . . . . . . . . -4.901 -0.360 2.920 20 . 35011 DNR HOP2 HOP2 HOP2 2HOP . H . . N 0 . . . 0 N N . . . . -2.116 . -8.974 . 16.130 . -4.684 -2.823 1.313 21 . 35011 DNR H5' H5' H5' 1H5* . H . . N 0 . . . 1 N N . . . . -2.630 . -6.429 . 17.716 . -1.971 -0.654 1.366 22 . 35011 DNR H5'' H5'' H5'' 2H5* . H . . N 0 . . . 0 N N . . . . -3.489 . -7.251 . 16.403 . -2.683 0.718 2.254 23 . 35011 DNR H4' H4' H4' H4* . H . . N 0 . . . 1 N N . . . . -4.660 . -5.225 . 17.266 . -0.644 0.753 3.736 24 . 35011 DNR H1' H1' H1' H1* . H . . N 0 . . . 1 N N . . . . -3.901 . -2.280 . 15.793 . 2.163 -0.604 2.054 25 . 35011 DNR H6 H6 H6 H6 . H . . N 0 . . . 1 N N . . . . -0.864 . -4.341 . 15.274 . -0.871 -2.335 1.453 26 . 35011 DNR HN3 HN3 HN3 HN3 . H . . N 0 . . . 1 N N . . . . -0.421 . 0.491 . 15.056 . 3.017 -4.226 -0.715 27 . 35011 DNR H41 H41 H41 H41 . H . . N 0 . . . 1 N N . . . . 1.833 . 0.257 . 14.671 . 0.511 -5.815 -1.789 28 . 35011 DNR H42 H42 H42 H42 . H . . N 0 . . . 1 N N . . . . 2.576 . -1.326 . 14.649 . 1.332 -6.567 -0.439 29 . 35011 DNR H5 H5 H5 H5 . H . . N 0 . . . 1 N N . . . . 1.346 . -3.360 . 14.919 . -1.040 -4.526 0.354 30 . 35011 DNR H2' H2' H2' 1H2* . H . . N 0 . . . 1 N N . . . . -2.839 . -4.348 . 13.921 . -0.003 -0.001 0.003 31 . 35011 DNR H2'' H2'' H2'' 2H2* . H . . N 0 . . . 0 N N . . . . -4.322 . -3.365 . 13.847 . 1.556 0.818 0.232 32 . 35011 DNR H3' H3' H3' H3* . H . . N 0 . . . 1 N N . . . . -4.291 . -5.978 . 14.608 . -0.722 1.941 1.236 33 . 35011 DNR HO3' HO3' HO3' H3T . H . . N 0 . . . 0 N Y . . . . -6.217 . -4.664 . 14.334 . 0.743 3.042 2.146 34 . 35011 DNR HOP3 HOP3 HOP3 3HOP . H . . N 0 . . . 0 N N . . . . -0.709 . -0.263 . 0.574 . -5.874 -0.475 2.871 35 . 35011 DNR stop_ loop_ _Chem_comp_bond.ID _Chem_comp_bond.Type _Chem_comp_bond.Value_order _Chem_comp_bond.Atom_ID_1 _Chem_comp_bond.Atom_ID_2 _Chem_comp_bond.Aromatic_flag _Chem_comp_bond.Stereo_config _Chem_comp_bond.Ordinal _Chem_comp_bond.Details _Chem_comp_bond.Entry_ID _Chem_comp_bond.Comp_ID 1 . DOUB P OP1 N N 1 . 35011 DNR 2 . SING P OP2 N N 2 . 35011 DNR 3 . SING P O5' N N 3 . 35011 DNR 4 . SING P OP3 N N 4 . 35011 DNR 5 . SING OP2 HOP2 N N 5 . 35011 DNR 6 . SING O5' C5' N N 6 . 35011 DNR 7 . SING C5' C4' N N 7 . 35011 DNR 8 . SING C5' H5' N N 8 . 35011 DNR 9 . SING C5' H5'' N N 9 . 35011 DNR 10 . SING C4' O4' N N 10 . 35011 DNR 11 . SING C4' C3' N N 11 . 35011 DNR 12 . SING C4' H4' N N 12 . 35011 DNR 13 . SING O4' C1' N N 13 . 35011 DNR 14 . SING C1' N1 N N 14 . 35011 DNR 15 . SING C1' C2' N N 15 . 35011 DNR 16 . SING C1' H1' N N 16 . 35011 DNR 17 . SING N1 C6 N N 17 . 35011 DNR 18 . SING N1 C2 N N 18 . 35011 DNR 19 . DOUB C6 C5 N N 19 . 35011 DNR 20 . SING C6 H6 N N 20 . 35011 DNR 21 . DOUB C2 O2 N N 21 . 35011 DNR 22 . SING C2 N3 N N 22 . 35011 DNR 23 . DOUB N3 C4 N N 23 . 35011 DNR 24 . SING N3 HN3 N N 24 . 35011 DNR 25 . SING C4 N4 N N 25 . 35011 DNR 26 . SING C4 C5 N N 26 . 35011 DNR 27 . SING N4 H41 N N 27 . 35011 DNR 28 . SING N4 H42 N N 28 . 35011 DNR 29 . SING C5 H5 N N 29 . 35011 DNR 30 . SING C2' C3' N N 30 . 35011 DNR 31 . SING C2' H2' N N 31 . 35011 DNR 32 . SING C2' H2'' N N 32 . 35011 DNR 33 . SING C3' O3' N N 33 . 35011 DNR 34 . SING C3' H3' N N 34 . 35011 DNR 35 . SING O3' HO3' N N 35 . 35011 DNR 36 . SING OP3 HOP3 N N 36 . 35011 DNR stop_ save_ ##################################### # Sample contents and methodology # ##################################### ######################## # Sample description # ######################## save_sample_1 _Sample.Sf_category sample _Sample.Sf_framecode sample_1 _Sample.Entry_ID 35011 _Sample.ID 1 _Sample.Name . _Sample.Type solution _Sample.Sub_type . _Sample.Details '10 mM NA- sodium phosphate, 50 mM NA- potassium chloride, .5 mM NA- iFRNA1 nucleotide, 90% H2O/10% D2O' _Sample.Aggregate_sample_number . _Sample.Solvent_system '90% H2O/10% D2O' _Sample.Preparation_date . _Sample.Preparation_expiration_date . _Sample.Polycrystallization_protocol . _Sample.Single_crystal_protocol . _Sample.Crystal_grow_apparatus . _Sample.Crystal_grow_atmosphere . _Sample.Crystal_grow_details . _Sample.Crystal_grow_method . _Sample.Crystal_grow_method_cit_ID . _Sample.Crystal_grow_pH . _Sample.Crystal_grow_pH_range . _Sample.Crystal_grow_pressure . _Sample.Crystal_grow_pressure_esd . _Sample.Crystal_grow_seeding . _Sample.Crystal_grow_seeding_cit_ID . _Sample.Crystal_grow_temp . _Sample.Crystal_grow_temp_details . _Sample.Crystal_grow_temp_esd . _Sample.Crystal_grow_time . _Sample.Oriented_sample_prep_protocol . _Sample.Lyophilization_cryo_protectant . _Sample.Storage_protocol . loop_ _Sample_component.ID _Sample_component.Mol_common_name _Sample_component.Isotopic_labeling _Sample_component.Assembly_ID _Sample_component.Assembly_label _Sample_component.Entity_ID _Sample_component.Entity_label _Sample_component.Product_ID _Sample_component.Type _Sample_component.Concentration_val _Sample_component.Concentration_val_min _Sample_component.Concentration_val_max _Sample_component.Concentration_val_units _Sample_component.Concentration_val_err _Sample_component.Vendor _Sample_component.Vendor_product_name _Sample_component.Vendor_product_code _Sample_component.Entry_ID _Sample_component.Sample_ID 1 'sodium phosphate' 'natural abundance' . . . . . . 10 . . mM . . . . 35011 1 2 'potassium chloride' 'natural abundance' . . . . . . 50 . . mM . . . . 35011 1 3 'iFRNA1 nucleotide' 'natural abundance' . . 1 $entity_1 . . 0.5 . . mM . . . . 35011 1 4 'iFRNA1 nucleotide' 'natural abundance' . . 2 $entity_2 . . 0.5 . . mM . . . . 35011 1 stop_ save_ ####################### # Sample conditions # ####################### save_sample_conditions_1 _Sample_condition_list.Sf_category sample_conditions _Sample_condition_list.Sf_framecode sample_conditions_1 _Sample_condition_list.Entry_ID 35011 _Sample_condition_list.ID 1 _Sample_condition_list.Name . _Sample_condition_list.Details . loop_ _Sample_condition_variable.Type _Sample_condition_variable.Val _Sample_condition_variable.Val_err _Sample_condition_variable.Val_units _Sample_condition_variable.Entry_ID _Sample_condition_variable.Sample_condition_list_ID 'ionic strength' 60 . mM 35011 1 pH 5 . pH 35011 1 pressure 1 . atm 35011 1 temperature 178 . K 35011 1 stop_ save_ ############################ # Computer software used # ############################ save_software_1 _Software.Sf_category software _Software.Sf_framecode software_1 _Software.Entry_ID 35011 _Software.ID 1 _Software.Type . _Software.Name TopSpin _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Bruker Biospin' . . 35011 1 stop_ loop_ _Task.Task _Task.Software_module _Task.Entry_ID _Task.Software_ID refinement . 35011 1 stop_ save_ save_software_2 _Software.Sf_category software _Software.Sf_framecode software_2 _Software.Entry_ID 35011 _Software.ID 2 _Software.Type . _Software.Name Amber _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' . . 35011 2 stop_ loop_ _Task.Task _Task.Software_module _Task.Entry_ID _Task.Software_ID 'structure calculation' . 35011 2 stop_ save_ save_software_3 _Software.Sf_category software _Software.Sf_framecode software_3 _Software.Entry_ID 35011 _Software.ID 3 _Software.Type . _Software.Name NMRFAM-SPARKY _Software.Version . _Software.DOI . _Software.Details . loop_ _Vendor.Name _Vendor.Address _Vendor.Electronic_address _Vendor.Entry_ID _Vendor.Software_ID 'National Magnetic Resonance Facility, University of Wisconsin Madison' . . 35011 3 stop_ loop_ _Task.Task _Task.Software_module _Task.Entry_ID _Task.Software_ID 'chemical shift assignment' . 35011 3 'peak picking' . 35011 3 stop_ save_ ######################### # Experimental detail # ######################### ################################## # NMR Spectrometer definitions # ################################## save_NMR_spectrometer_1 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_1 _NMR_spectrometer.Entry_ID 35011 _NMR_spectrometer.ID 1 _NMR_spectrometer.Name . _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model 'AVANCE NEO' _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 600 save_ save_NMR_spectrometer_2 _NMR_spectrometer.Sf_category NMR_spectrometer _NMR_spectrometer.Sf_framecode NMR_spectrometer_2 _NMR_spectrometer.Entry_ID 35011 _NMR_spectrometer.ID 2 _NMR_spectrometer.Name . _NMR_spectrometer.Details . _NMR_spectrometer.Manufacturer Bruker _NMR_spectrometer.Model 'AVANCE NEO' _NMR_spectrometer.Serial_number . _NMR_spectrometer.Field_strength 800 save_ save_NMR_spectrometer_list _NMR_spectrometer_list.Sf_category NMR_spectrometer_list _NMR_spectrometer_list.Sf_framecode NMR_spectrometer_list _NMR_spectrometer_list.Entry_ID 35011 _NMR_spectrometer_list.ID 1 _NMR_spectrometer_list.Name . loop_ _NMR_spectrometer_view.ID _NMR_spectrometer_view.Name _NMR_spectrometer_view.Manufacturer _NMR_spectrometer_view.Model _NMR_spectrometer_view.Serial_number _NMR_spectrometer_view.Field_strength _NMR_spectrometer_view.Details _NMR_spectrometer_view.Citation_ID _NMR_spectrometer_view.Citation_label _NMR_spectrometer_view.Entry_ID _NMR_spectrometer_view.NMR_spectrometer_list_ID 1 NMR_spectrometer_1 Bruker 'AVANCE NEO' . 600 . . . 35011 1 2 NMR_spectrometer_2 Bruker 'AVANCE NEO' . 800 . . . 35011 1 stop_ save_ ############################# # NMR applied experiments # ############################# save_experiment_list _Experiment_list.Sf_category experiment_list _Experiment_list.Sf_framecode experiment_list _Experiment_list.Entry_ID 35011 _Experiment_list.ID 1 _Experiment_list.Details . loop_ _Experiment.ID _Experiment.Name _Experiment.Raw_data_flag _Experiment.NUS_flag _Experiment.Interleaved_flag _Experiment.NMR_spec_expt_ID _Experiment.NMR_spec_expt_label _Experiment.MS_expt_ID _Experiment.MS_expt_label _Experiment.SAXS_expt_ID _Experiment.SAXS_expt_label _Experiment.FRET_expt_ID _Experiment.FRET_expt_label _Experiment.EMR_expt_ID _Experiment.EMR_expt_label _Experiment.Sample_ID _Experiment.Sample_label _Experiment.Sample_state _Experiment.Sample_volume _Experiment.Sample_volume_units _Experiment.Sample_condition_list_ID _Experiment.Sample_condition_list_label _Experiment.Sample_spinning_rate _Experiment.Sample_angle _Experiment.NMR_tube_type _Experiment.NMR_spectrometer_ID _Experiment.NMR_spectrometer_label _Experiment.NMR_spectrometer_probe_ID _Experiment.NMR_spectrometer_probe_label _Experiment.NMR_spectral_processing_ID _Experiment.NMR_spectral_processing_label _Experiment.Mass_spectrometer_ID _Experiment.Mass_spectrometer_label _Experiment.Xray_instrument_ID _Experiment.Xray_instrument_label _Experiment.Fluorescence_instrument_ID _Experiment.Fluorescence_instrument_label _Experiment.EMR_instrument_ID _Experiment.EMR_instrument_label _Experiment.Chromatographic_system_ID _Experiment.Chromatographic_system_label _Experiment.Chromatographic_column_ID _Experiment.Chromatographic_column_label _Experiment.Details _Experiment.Entry_ID _Experiment.Experiment_list_ID 1 '2D NOESY' no . . . . . . . . . . . . 1 $sample_1 anisotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 35011 1 2 '2D HOESY' no . . . . . . . . . . . . 1 $sample_1 anisotropic . . 1 $sample_conditions_1 . . . 1 $NMR_spectrometer_1 . . . . . . . . . . . . . . . . . 35011 1 3 '2D TOCSY' no . . . . . . . . . . . . 1 $sample_1 anisotropic . . 1 $sample_conditions_1 . . . 2 $NMR_spectrometer_2 . . . . . . . . . . . . . . . . . 35011 1 stop_ save_ #################### # NMR parameters # #################### ############################## # Assigned chemical shifts # ############################## ################################ # Chemical shift referencing # ################################ save_chem_shift_reference_1 _Chem_shift_reference.Sf_category chem_shift_reference _Chem_shift_reference.Sf_framecode chem_shift_reference_1 _Chem_shift_reference.Entry_ID 35011 _Chem_shift_reference.ID 1 _Chem_shift_reference.Name . _Chem_shift_reference.Details . loop_ _Chem_shift_ref.Atom_type _Chem_shift_ref.Atom_isotope_number _Chem_shift_ref.Mol_common_name _Chem_shift_ref.Atom_group _Chem_shift_ref.Concentration_val _Chem_shift_ref.Concentration_units _Chem_shift_ref.Solvent _Chem_shift_ref.Rank _Chem_shift_ref.Chem_shift_units _Chem_shift_ref.Chem_shift_val _Chem_shift_ref.Ref_method _Chem_shift_ref.Ref_type _Chem_shift_ref.Indirect_shift_ratio _Chem_shift_ref.External_ref_loc _Chem_shift_ref.External_ref_sample_geometry _Chem_shift_ref.External_ref_axis _Chem_shift_ref.Ref_correction_type _Chem_shift_ref.Correction_val _Chem_shift_ref.Entry_ID _Chem_shift_ref.Chem_shift_reference_ID F 19 DSS fluorine . . . . ppm 0.000 external indirect 0.941449 . . . . . 35011 1 H 1 DSS 'methyl protons' . . . . ppm 0.000 internal direct 1.0 . . . . . 35011 1 stop_ save_ ################################### # Assigned chemical shift lists # ################################### ################################################################### # Chemical Shift Ambiguity Index Value Definitions # # # # The values other than 1 are used for those atoms with different # # chemical shifts that cannot be assigned to stereospecific atoms # # or to specific residues or chains. # # # # Index Value Definition # # # # 1 Unique (including isolated methyl protons, # # geminal atoms, and geminal methyl # # groups with identical chemical shifts) # # (e.g. ILE HD11, HD12, HD13 protons) # # 2 Ambiguity of geminal atoms or geminal methyl # # proton groups (e.g. ASP HB2 and HB3 # # protons, LEU CD1 and CD2 carbons, or # # LEU HD11, HD12, HD13 and HD21, HD22, # # HD23 methyl protons) # # 3 Aromatic atoms on opposite sides of # # symmetrical rings (e.g. TYR HE1 and HE2 # # protons) # # 4 Intraresidue ambiguities (e.g. LYS HG and # # HD protons or TRP HZ2 and HZ3 protons) # # 5 Interresidue ambiguities (LYS 12 vs. LYS 27) # # 6 Intermolecular ambiguities (e.g. ASP 31 CA # # in monomer 1 and ASP 31 CA in monomer 2 # # of an asymmetrical homodimer, duplex # # DNA assignments, or other assignments # # that may apply to atoms in one or more # # molecule in the molecular assembly) # # 9 Ambiguous, specific ambiguity not defined # # # ################################################################### save_assigned_chemical_shifts_1 _Assigned_chem_shift_list.Sf_category assigned_chemical_shifts _Assigned_chem_shift_list.Sf_framecode assigned_chemical_shifts_1 _Assigned_chem_shift_list.Entry_ID 35011 _Assigned_chem_shift_list.ID 1 _Assigned_chem_shift_list.Name . _Assigned_chem_shift_list.Sample_condition_list_ID 1 _Assigned_chem_shift_list.Sample_condition_list_label $sample_conditions_1 _Assigned_chem_shift_list.Chem_shift_reference_ID 1 _Assigned_chem_shift_list.Chem_shift_reference_label $chem_shift_reference_1 _Assigned_chem_shift_list.Chem_shift_1H_err . _Assigned_chem_shift_list.Chem_shift_13C_err . _Assigned_chem_shift_list.Chem_shift_15N_err . _Assigned_chem_shift_list.Chem_shift_31P_err . _Assigned_chem_shift_list.Chem_shift_2H_err . _Assigned_chem_shift_list.Chem_shift_19F_err . _Assigned_chem_shift_list.Error_derivation_method . _Assigned_chem_shift_list.Details . _Assigned_chem_shift_list.Text_data_format . _Assigned_chem_shift_list.Text_data . loop_ _Chem_shift_experiment.Experiment_ID _Chem_shift_experiment.Experiment_name _Chem_shift_experiment.Sample_ID _Chem_shift_experiment.Sample_label _Chem_shift_experiment.Sample_state _Chem_shift_experiment.Entry_ID _Chem_shift_experiment.Assigned_chem_shift_list_ID 1 '2D NOESY' . . . 35011 1 2 '2D HOESY' . . . 35011 1 3 '2D TOCSY' . . . 35011 1 stop_ loop_ _Atom_chem_shift.ID _Atom_chem_shift.Assembly_atom_ID _Atom_chem_shift.Entity_assembly_ID _Atom_chem_shift.Entity_assembly_asym_ID _Atom_chem_shift.Entity_ID _Atom_chem_shift.Comp_index_ID _Atom_chem_shift.Seq_ID _Atom_chem_shift.Comp_ID _Atom_chem_shift.Atom_ID _Atom_chem_shift.Atom_type _Atom_chem_shift.Atom_isotope_number _Atom_chem_shift.Val _Atom_chem_shift.Val_err _Atom_chem_shift.Assign_fig_of_merit _Atom_chem_shift.Ambiguity_code _Atom_chem_shift.Ambiguity_set_ID _Atom_chem_shift.Occupancy _Atom_chem_shift.Resonance_ID _Atom_chem_shift.Auth_entity_assembly_ID _Atom_chem_shift.Auth_asym_ID _Atom_chem_shift.Auth_seq_ID _Atom_chem_shift.Auth_comp_ID _Atom_chem_shift.Auth_atom_ID _Atom_chem_shift.Details _Atom_chem_shift.Entry_ID _Atom_chem_shift.Assigned_chem_shift_list_ID 1 . 3 . 2 1 1 DT H1' H 1 6.338 0.00 . 1 . . . . C 1 DT H1' . 35011 1 2 . 3 . 2 1 1 DT H2' H 1 2.640 0.00 . . . . . . C 1 DT H2' . 35011 1 3 . 3 . 2 1 1 DT H2'' H 1 2.179 0.00 . . . . . . C 1 DT H2'' . 35011 1 4 . 3 . 2 1 1 DT H3 H 1 11.468 0.00 . 1 . . . . C 1 DT H3 . 35011 1 5 . 3 . 2 1 1 DT H3' H 1 4.840 0.00 . 1 . . . . C 1 DT H3' . 35011 1 6 . 3 . 2 1 1 DT H4' H 1 4.034 0.00 . 1 . . . . C 1 DT H4' . 35011 1 7 . 3 . 2 1 1 DT H5' H 1 3.864 0.00 . . . . . . C 1 DT H5' . 35011 1 8 . 3 . 2 1 1 DT H5'' H 1 3.959 0.01 . . . . . . C 1 DT H5'' . 35011 1 9 . 3 . 2 1 1 DT H6 H 1 7.647 0.00 . 1 . . . . C 1 DT H6 . 35011 1 10 . 3 . 2 1 1 DT H71 H 1 1.772 0.00 . 1 . . . . C 1 DT H71 . 35011 1 11 . 3 . 2 2 2 DNR H1' H 1 6.484 0.00 . . . . . . C 2 DNR H1' . 35011 1 12 . 3 . 2 2 2 DNR H2' H 1 2.084 0.00 . . . . . . C 2 DNR H2' . 35011 1 13 . 3 . 2 2 2 DNR H3' H 1 4.853 0.00 . . . . . . C 2 DNR H3' . 35011 1 14 . 3 . 2 2 2 DNR H4' H 1 4.170 0.00 . . . . . . C 2 DNR H4' . 35011 1 15 . 3 . 2 2 2 DNR H5 H 1 5.944 0.00 . . . . . . C 2 DNR H5 . 35011 1 16 . 3 . 2 2 2 DNR H6 H 1 7.918 0.00 . . . . . . C 2 DNR H6 . 35011 1 17 . 3 . 2 2 2 DNR H41 H 1 9.268 0.00 . . . . . . C 2 DNR H41 . 35011 1 18 . 3 . 2 2 2 DNR H42 H 1 8.254 0.00 . . . . . . C 2 DNR H42 . 35011 1 19 . 3 . 2 2 2 DNR HN3 H 1 15.865 0.00 . 1 . . . . C 2 DNR HN3 . 35011 1 20 . 3 . 2 3 3 DNR H1' H 1 6.384 0.01 . . . . . . C 3 DNR H1' . 35011 1 21 . 3 . 2 3 3 DNR H2' H 1 2.017 0.00 . . . . . . C 3 DNR H2' . 35011 1 22 . 3 . 2 3 3 DNR H3' H 1 4.822 0.00 . . . . . . C 3 DNR H3' . 35011 1 23 . 3 . 2 3 3 DNR H4' H 1 4.104 0.01 . . . . . . C 3 DNR H4' . 35011 1 24 . 3 . 2 3 3 DNR H5 H 1 5.959 0.00 . . . . . . C 3 DNR H5 . 35011 1 25 . 3 . 2 3 3 DNR H6 H 1 7.678 0.00 . . . . . . C 3 DNR H6 . 35011 1 26 . 3 . 2 3 3 DNR H41 H 1 9.242 0.00 . . . . . . C 3 DNR H41 . 35011 1 27 . 3 . 2 3 3 DNR H42 H 1 8.208 0.00 . . . . . . C 3 DNR H42 . 35011 1 28 . 3 . 2 3 3 DNR HN3 H 1 15.582 0.00 . 1 . . . . C 3 DNR HN3 . 35011 1 29 . 3 . 2 4 4 CFZ H1' H 1 6.518 0.00 . 1 . . . . C 4 CFZ H1' . 35011 1 30 . 3 . 2 4 4 CFZ H2' H 1 4.934 0.00 . 1 . . . . C 4 CFZ H2' . 35011 1 31 . 3 . 2 4 4 CFZ H3' H 1 4.631 0.00 . 1 . . . . C 4 CFZ H3' . 35011 1 32 . 3 . 2 4 4 CFZ H4' H 1 4.334 0.00 . 1 . . . . C 4 CFZ H4' . 35011 1 33 . 3 . 2 4 4 CFZ H5 H 1 5.962 0.00 . 1 . . . . C 4 CFZ H5 . 35011 1 34 . 3 . 2 4 4 CFZ H5'A H 1 4.459 0.00 . . . . . . C 4 CFZ H5'A . 35011 1 35 . 3 . 2 4 4 CFZ H6 H 1 7.498 0.00 . 1 . . . . C 4 CFZ H6 . 35011 1 36 . 3 . 2 4 4 CFZ F2' F 19 -115.124 0.00 . . . . . . C 4 CFZ F2' . 35011 1 37 . 3 . 2 4 4 CFZ HN3 H 1 15.288 0.00 . . . . . . C 4 CFZ HN3 . 35011 1 38 . 3 . 2 4 4 CFZ HN4 H 1 9.087 0.00 . . . . . . C 4 CFZ HN4 . 35011 1 39 . 3 . 2 4 4 CFZ HN4A H 1 8.639 0.00 . . . . . . C 4 CFZ HN4A . 35011 1 40 . 3 . 2 5 5 DC H1' H 1 6.350 0.00 . . . . . . C 5 DC H1' . 35011 1 41 . 3 . 2 5 5 DC H2' H 1 2.163 0.00 . . . . . . C 5 DC H2' . 35011 1 42 . 3 . 2 5 5 DC H3' H 1 4.650 0.00 . . . . . . C 5 DC H3' . 35011 1 43 . 3 . 2 5 5 DC H4' H 1 4.045 0.00 . . . . . . C 5 DC H4' . 35011 1 44 . 3 . 2 5 5 DC H5 H 1 5.923 0.00 . . . . . . C 5 DC H5 . 35011 1 45 . 3 . 2 5 5 DC H6 H 1 7.612 0.00 . . . . . . C 5 DC H6 . 35011 1 46 . 3 . 2 5 5 DC H41 H 1 9.316 0.00 . . . . . . C 5 DC H41 . 35011 1 47 . 3 . 2 5 5 DC H42 H 1 8.370 0.00 . . . . . . C 5 DC H42 . 35011 1 48 . 3 . 2 5 5 DC HN3 H 1 15.656 0.00 . 1 . . . . C 5 DC HN3 . 35011 1 49 . 3 . 2 6 6 DNR H1' H 1 6.192 0.00 . . . . . . C 6 DNR H1' . 35011 1 50 . 3 . 2 6 6 DNR H2' H 1 2.202 0.01 . . . . . . C 6 DNR H2' . 35011 1 51 . 3 . 2 6 6 DNR H3' H 1 4.301 0.00 . . . . . . C 6 DNR H3' . 35011 1 52 . 3 . 2 6 6 DNR H4' H 1 3.948 0.00 . . . . . . C 6 DNR H4' . 35011 1 53 . 3 . 2 6 6 DNR H5 H 1 5.972 0.00 . . . . . . C 6 DNR H5 . 35011 1 54 . 3 . 2 6 6 DNR H5' H 1 4.215 0.00 . . . . . . C 6 DNR H5' . 35011 1 55 . 3 . 2 6 6 DNR H5'' H 1 4.032 0.00 . . . . . . C 6 DNR H5'' . 35011 1 56 . 3 . 2 6 6 DNR H6 H 1 7.740 0.00 . . . . . . C 6 DNR H6 . 35011 1 57 . 3 . 2 6 6 DNR H41 H 1 9.197 0.00 . . . . . . C 6 DNR H41 . 35011 1 58 . 3 . 2 6 6 DNR H42 H 1 8.307 0.00 . . . . . . C 6 DNR H42 . 35011 1 59 . 3 . 2 6 6 DNR HN3 H 1 15.655 0.00 . 1 . . . . C 6 DNR HN3 . 35011 1 stop_ save_