data_7NBK # _entry.id 7NBK # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.392 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 7NBK pdb_00007nbk 10.2210/pdb7nbk/pdb WWPDB D_1292113667 ? ? BMRB 34594 ? 10.13018/BMR34594 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2021-04-07 2 'Structure model' 1 1 2024-05-15 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Data collection' 2 2 'Structure model' 'Database references' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 2 'Structure model' chem_comp_atom 2 2 'Structure model' chem_comp_bond 3 2 'Structure model' database_2 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 2 'Structure model' '_database_2.pdbx_DOI' 2 2 'Structure model' '_database_2.pdbx_database_accession' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 7NBK _pdbx_database_status.recvd_initial_deposition_date 2021-01-27 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type PDB 'Other structure with the same modification' 7NBL unspecified BMRB ;Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification ; 34594 unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Cabrero, C.' 1 ? 'Martin-Pintado, N.' 2 ? 'Mazzini, S.' 3 ? 'Gargallo, R.' 4 ? 'Eritja, R.' 5 ? 'Avino, A.' 6 ? 'Gonzalez, C.' 7 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country GE _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Chemistry _citation.journal_id_ASTM ? _citation.journal_id_CSD ? _citation.journal_id_ISSN 0947-6539 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume ? _citation.language ? _citation.page_first ? _citation.page_last ? _citation.title 'Structural Effects of Incorporation of 2 -Deoxy-2 2 -difluorodeoxycytidine (Gemcitabine) in A- and B-form Duplexes.' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/chem.202100503 _citation.pdbx_database_id_PubMed 33772916 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Cabrero, C.' 1 ? primary 'Martin-Pintado, N.' 2 ? primary 'Mazzini, S.' 3 ? primary 'Gargallo, R.' 4 ? primary 'Eritja, R.' 5 ? primary 'Avino, A.' 6 ? primary 'Gonzalez, C.' 7 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3') ; _entity.formula_weight 1845.198 _entity.pdbx_number_of_molecules 2 _entity.pdbx_ec ? _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.details ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(U7B)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DC n 1 2 DG n 1 3 DT n 1 4 DA n 1 5 U7B n 1 6 DG n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num 1 _pdbx_entity_src_syn.pdbx_end_seq_num 6 _pdbx_entity_src_syn.organism_scientific 'synthetic construct' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 32630 _pdbx_entity_src_syn.details ? # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 U7B 'DNA linking' n "2'-deoxy-2'2'-difluorodeoxycytidine" ;[(2~{R},3~{R},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-4,4-bis(fluoranyl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite ; 'C9 H12 F2 N3 O7 P' 343.178 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 DC 1 1 1 DC DC A . n A 1 2 DG 2 2 2 DG DG A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DA 4 4 4 DA DA A . n A 1 5 U7B 5 5 5 U7B FFC A . n A 1 6 DG 6 6 6 DG DG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 DG 2 8 8 DG DG B . n B 1 3 DT 3 9 9 DT DT B . n B 1 4 DA 4 10 10 DA DA B . n B 1 5 U7B 5 11 11 U7B FFC B . n B 1 6 DG 6 12 12 DG DG B . n # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 7NBK _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7NBK _struct.title ;Solution structure of DNA duplex containing a 2'-deoxy-2'2'-difluorodeoxycytidine (gemcitabine) modification ; _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 7NBK _struct_keywords.text 'Fluorine modification, modified DNA, gemcitabine, DNA' _struct_keywords.pdbx_keywords DNA # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7NBK _struct_ref.pdbx_db_accession 7NBK _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 7NBK A 1 ? 6 ? 7NBK 1 ? 6 ? 1 6 2 1 7NBK B 1 ? 6 ? 7NBK 7 ? 12 ? 7 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 590 ? 1 MORE -2 ? 1 'SSA (A^2)' 2520 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support none _pdbx_struct_assembly_auth_evidence.details ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A DA 4 "O3'" ? ? ? 1_555 A U7B 5 P ? ? A DA 4 A U7B 5 1_555 ? ? ? ? ? ? ? 1.624 ? ? covale2 covale one ? A U7B 5 "O3'" ? ? ? 1_555 A DG 6 P ? ? A U7B 5 A DG 6 1_555 ? ? ? ? ? ? ? 1.623 ? ? covale3 covale both ? B DA 4 "O3'" ? ? ? 1_555 B U7B 5 P ? ? B DA 10 B U7B 11 1_555 ? ? ? ? ? ? ? 1.629 ? ? covale4 covale one ? B U7B 5 "O3'" ? ? ? 1_555 B DG 6 P ? ? B U7B 11 B DG 12 1_555 ? ? ? ? ? ? ? 1.607 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 6 N1 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 6 O6 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 6 N2 ? ? A DC 1 B DG 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B U7B 5 N3 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B U7B 5 O2 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B U7B 5 N4 ? ? A DG 2 B U7B 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A U7B 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A U7B 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A U7B 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A U7B 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DG 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DG 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DG 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? hydrog ? ? # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 112.14 108.30 3.84 0.30 N 2 1 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.32 108.30 4.02 0.30 N 3 1 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.86 108.30 2.56 0.30 N 4 1 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.74 122.90 -4.16 0.60 N 5 1 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.00 108.30 2.70 0.30 N 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.92 108.30 3.62 0.30 N 7 1 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 113.61 108.30 5.31 0.30 N 8 1 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.97 108.30 2.67 0.30 N 9 1 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.96 117.00 -3.04 0.50 N 10 1 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.70 118.60 -3.90 0.60 N 11 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.88 108.30 3.58 0.30 N 12 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.24 108.30 2.94 0.30 N 13 2 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.23 108.30 3.93 0.30 N 14 2 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.37 108.30 2.07 0.30 N 15 2 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.95 122.90 -3.95 0.60 N 16 2 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.90 117.00 -3.10 0.50 N 17 2 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 111.27 108.30 2.97 0.30 N 18 2 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.01 108.30 2.71 0.30 N 19 2 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.58 108.30 3.28 0.30 N 20 2 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.23 108.30 2.93 0.30 N 21 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.54 108.30 2.24 0.30 N 22 3 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.49 108.30 3.19 0.30 N 23 3 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.46 108.30 2.16 0.30 N 24 3 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.76 117.00 -3.24 0.50 N 25 3 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.59 118.60 -4.01 0.60 N 26 3 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.17 108.30 2.87 0.30 N 27 3 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.01 108.30 3.71 0.30 N 28 3 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.19 108.30 1.89 0.30 N 29 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.21 108.30 2.91 0.30 N 30 4 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 113.56 108.30 5.26 0.30 N 31 4 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.29 108.30 2.99 0.30 N 32 4 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.84 117.00 -3.16 0.50 N 33 4 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.67 118.60 -3.93 0.60 N 34 4 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.81 108.30 2.51 0.30 N 35 4 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.70 108.30 2.40 0.30 N 36 4 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.60 108.30 4.30 0.30 N 37 4 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 111.02 108.30 2.72 0.30 N 38 4 C6 B DT 9 ? ? C5 B DT 9 ? ? C7 B DT 9 ? ? 118.16 122.90 -4.74 0.60 N 39 4 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.94 118.60 -3.66 0.60 N 40 4 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 111.87 108.30 3.57 0.30 N 41 5 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.24 108.30 1.94 0.30 N 42 5 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.38 108.30 3.08 0.30 N 43 5 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.54 108.30 2.24 0.30 N 44 5 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 112.89 108.30 4.59 0.30 N 45 5 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.58 108.30 4.28 0.30 N 46 5 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.94 117.00 -3.06 0.50 N 47 5 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.81 118.60 -3.79 0.60 N 48 5 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.29 108.30 1.99 0.30 N 49 6 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.73 108.30 2.43 0.30 N 50 6 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.46 108.30 3.16 0.30 N 51 6 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.23 108.30 1.93 0.30 N 52 6 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.87 117.00 -3.13 0.50 N 53 6 N1 A DA 4 ? ? C6 A DA 4 ? ? N6 A DA 4 ? ? 114.24 118.60 -4.36 0.60 N 54 6 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.41 108.30 3.11 0.30 N 55 6 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.36 108.30 4.06 0.30 N 56 6 "O4'" B DT 9 ? ? "C1'" B DT 9 ? ? N1 B DT 9 ? ? 110.47 108.30 2.17 0.30 N 57 6 C4 B DA 10 ? ? C5 B DA 10 ? ? C6 B DA 10 ? ? 113.78 117.00 -3.22 0.50 N 58 6 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.62 118.60 -3.98 0.60 N 59 7 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.59 108.30 2.29 0.30 N 60 7 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 112.46 108.30 4.16 0.30 N 61 7 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 111.11 108.30 2.81 0.30 N 62 7 C4 A DA 4 ? ? C5 A DA 4 ? ? C6 A DA 4 ? ? 113.92 117.00 -3.08 0.50 N 63 7 "O4'" A DG 6 ? ? "C1'" A DG 6 ? ? N9 A DG 6 ? ? 110.34 108.30 2.04 0.30 N 64 7 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 111.31 108.30 3.01 0.30 N 65 7 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.68 108.30 4.38 0.30 N 66 8 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.94 108.30 2.64 0.30 N 67 8 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.51 108.30 3.21 0.30 N 68 8 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.63 108.30 2.33 0.30 N 69 8 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 112.22 108.30 3.92 0.30 N 70 8 N1 B DA 10 ? ? C6 B DA 10 ? ? N6 B DA 10 ? ? 114.41 118.60 -4.19 0.60 N 71 8 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.19 108.30 1.89 0.30 N 72 9 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 110.14 108.30 1.84 0.30 N 73 9 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.22 108.30 2.92 0.30 N 74 9 "O4'" A DT 3 ? ? "C1'" A DT 3 ? ? N1 A DT 3 ? ? 110.32 108.30 2.02 0.30 N 75 9 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.81 108.30 2.51 0.30 N 76 9 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.66 108.30 3.36 0.30 N 77 10 "O4'" A DG 2 ? ? "C1'" A DG 2 ? ? N9 A DG 2 ? ? 111.56 108.30 3.26 0.30 N 78 10 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.86 122.90 -4.04 0.60 N 79 10 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 110.61 108.30 2.31 0.30 N 80 10 "O4'" B DG 8 ? ? "C1'" B DG 8 ? ? N9 B DG 8 ? ? 111.02 108.30 2.72 0.30 N 81 10 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.51 108.30 2.21 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 2 ? ? 0.058 'SIDE CHAIN' 2 1 DC B 7 ? ? 0.065 'SIDE CHAIN' 3 1 DT B 9 ? ? 0.081 'SIDE CHAIN' 4 2 DC A 1 ? ? 0.076 'SIDE CHAIN' 5 2 DG A 6 ? ? 0.050 'SIDE CHAIN' 6 2 DC B 7 ? ? 0.067 'SIDE CHAIN' 7 3 DG B 8 ? ? 0.055 'SIDE CHAIN' 8 4 DG A 2 ? ? 0.056 'SIDE CHAIN' 9 4 DC B 7 ? ? 0.083 'SIDE CHAIN' 10 6 DC A 1 ? ? 0.078 'SIDE CHAIN' 11 7 DC B 7 ? ? 0.085 'SIDE CHAIN' 12 8 DC B 7 ? ? 0.106 'SIDE CHAIN' 13 9 DC A 1 ? ? 0.069 'SIDE CHAIN' 14 9 DC B 7 ? ? 0.064 'SIDE CHAIN' 15 10 DC A 1 ? ? 0.081 'SIDE CHAIN' 16 10 DC B 7 ? ? 0.103 'SIDE CHAIN' # _pdbx_entry_details.entry_id 7NBK _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_nmr_ensemble.entry_id 7NBK _pdbx_nmr_ensemble.conformers_calculated_total_number 10 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'all calculated structures submitted' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 7NBK _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 ;0.5 M DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 90% H2O/10% D2O ; '90% H2O/10% D2O' DiFs_Duplex solution ? 2 ;0.5 mM DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3'), 25 mM sodium phosphate, 100 mM sodium chloride, 0.5 % v/v DSS, 100% D2O ; '100% D2O' DiFs_Duplex_D2O solution ? # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 ;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3') ; 0.5 ? M 'natural abundance' 1 'sodium phosphate' 25 ? mM 'natural abundance' 1 'sodium chloride' 100 ? mM 'natural abundance' 1 DSS 0.5 ? '% v/v' 'natural abundance' 2 ;DNA (5'-D(*CP*GP*TP*AP*(FFC)P*G)-3') ; 0.5 ? mM 'natural abundance' 2 'sodium phosphate' 25 ? mM 'natural abundance' 2 'sodium chloride' 100 ? mM 'natural abundance' 2 DSS 0.5 ? '% v/v' 'natural abundance' # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 278 atm 1 7 125 ? ? mM T5 ? pH ? ? K 2 298 atm 1 7 125 ? ? mM T25 ? pH ? ? K # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-1H NOESY' 1 isotropic 2 1 1 '2D 1H-1H TOCSY' 1 isotropic 3 2 2 '2D 1H-1H COSY' 1 isotropic 4 2 2 '2D 1H-1H NOESY' 1 isotropic 5 2 2 '2D 1H-1H TOCSY' 1 isotropic # _pdbx_nmr_refine.entry_id 7NBK _pdbx_nmr_refine.method 'molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 5 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 collection TopSpin ? 'Bruker Biospin' 2 processing TopSpin ? 'Bruker Biospin' 3 'chemical shift assignment' NMRFAM-SPARKY ? 'Goddard & Kneller' 4 'structure calculation' Amber 18 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' 5 refinement Amber 18 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' 6 'data analysis' MOLMOL ? 'Koradi, Billeter and Wuthrich' 7 'data analysis' 3DNA ? 'Lu & Olson' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 U7B P P N N 144 U7B "C5'" C N N 145 U7B "O5'" O N N 146 U7B "C4'" C N R 147 U7B "O4'" O N N 148 U7B "C3'" C N R 149 U7B "O3'" O N N 150 U7B "C2'" C N N 151 U7B "C1'" C N R 152 U7B N1 N N N 153 U7B C2 C N N 154 U7B O2 O N N 155 U7B N3 N N N 156 U7B C4 C N N 157 U7B N4 N N N 158 U7B C5 C N N 159 U7B C6 C N N 160 U7B OP1 O N N 161 U7B OP2 O N N 162 U7B F1 F N N 163 U7B F2 F N N 164 U7B "H5''" H N N 165 U7B "H5'" H N N 166 U7B "H4'" H N N 167 U7B "H3'" H N N 168 U7B H1 H N N 169 U7B "H1'" H N N 170 U7B H42 H N N 171 U7B H41 H N N 172 U7B H5 H N N 173 U7B H6 H N N 174 U7B H3 H N N 175 U7B OP3 O N N 176 U7B H2 H N N 177 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 U7B OP1 P doub N N 150 U7B P "O5'" sing N N 151 U7B P OP2 sing N N 152 U7B "C5'" "C4'" sing N N 153 U7B "C5'" "O5'" sing N N 154 U7B "O4'" "C4'" sing N N 155 U7B "O4'" "C1'" sing N N 156 U7B "C4'" "C3'" sing N N 157 U7B "C1'" N1 sing N N 158 U7B "C1'" "C2'" sing N N 159 U7B N1 C6 sing N N 160 U7B N1 C2 sing N N 161 U7B O2 C2 doub N N 162 U7B C6 C5 doub N N 163 U7B C2 N3 sing N N 164 U7B C5 C4 sing N N 165 U7B N3 C4 doub N N 166 U7B "C3'" "O3'" sing N N 167 U7B "C3'" "C2'" sing N N 168 U7B C4 N4 sing N N 169 U7B "C2'" F1 sing N N 170 U7B "C2'" F2 sing N N 171 U7B "C5'" "H5''" sing N N 172 U7B "C5'" "H5'" sing N N 173 U7B "C4'" "H4'" sing N N 174 U7B "C3'" "H3'" sing N N 175 U7B "O3'" H1 sing N N 176 U7B "C1'" "H1'" sing N N 177 U7B N4 H42 sing N N 178 U7B N4 H41 sing N N 179 U7B C5 H5 sing N N 180 U7B C6 H6 sing N N 181 U7B OP2 H3 sing N N 182 U7B P OP3 sing N N 183 U7B OP3 H2 sing N N 184 # _ndb_struct_conf_na.entry_id 7NBK _ndb_struct_conf_na.feature 'double helix' # loop_ _ndb_struct_na_base_pair.model_number _ndb_struct_na_base_pair.i_label_asym_id _ndb_struct_na_base_pair.i_label_comp_id _ndb_struct_na_base_pair.i_label_seq_id _ndb_struct_na_base_pair.i_symmetry _ndb_struct_na_base_pair.j_label_asym_id _ndb_struct_na_base_pair.j_label_comp_id _ndb_struct_na_base_pair.j_label_seq_id _ndb_struct_na_base_pair.j_symmetry _ndb_struct_na_base_pair.shear _ndb_struct_na_base_pair.stretch _ndb_struct_na_base_pair.stagger _ndb_struct_na_base_pair.buckle _ndb_struct_na_base_pair.propeller _ndb_struct_na_base_pair.opening _ndb_struct_na_base_pair.pair_number _ndb_struct_na_base_pair.pair_name _ndb_struct_na_base_pair.i_auth_asym_id _ndb_struct_na_base_pair.i_auth_seq_id _ndb_struct_na_base_pair.i_PDB_ins_code _ndb_struct_na_base_pair.j_auth_asym_id _ndb_struct_na_base_pair.j_auth_seq_id _ndb_struct_na_base_pair.j_PDB_ins_code _ndb_struct_na_base_pair.hbond_type_28 _ndb_struct_na_base_pair.hbond_type_12 1 A DC 1 1_555 B DG 6 1_555 0.391 -0.261 0.238 -7.353 -5.922 -0.877 1 A_DC1:DG12_B A 1 ? B 12 ? 19 1 1 A DG 2 1_555 B U7B 5 1_555 -0.310 -0.242 0.494 14.249 1.123 -0.073 2 A_DG2:U7B11_B A 2 ? B 11 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 -0.056 -0.108 -0.015 18.674 1.271 2.697 3 A_DT3:DA10_B A 3 ? B 10 ? 20 1 1 A DA 4 1_555 B DT 3 1_555 0.071 -0.165 -0.264 3.685 -5.720 -0.279 4 A_DA4:DT9_B A 4 ? B 9 ? 20 1 1 A U7B 5 1_555 B DG 2 1_555 0.375 -0.261 -0.087 -6.927 -1.915 -0.404 5 A_U7B5:DG8_B A 5 ? B 8 ? 19 1 1 A DG 6 1_555 B DC 1 1_555 -0.334 -0.254 0.020 6.401 -8.494 -1.172 6 A_DG6:DC7_B A 6 ? B 7 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 6 1_555 A DG 2 1_555 B U7B 5 1_555 1.094 0.716 3.295 -3.340 14.249 26.544 -1.650 -2.805 3.112 28.450 6.669 30.248 1 AA_DC1DG2:U7B11DG12_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A DG 2 1_555 B U7B 5 1_555 A DT 3 1_555 B DA 4 1_555 -0.384 -1.132 3.342 2.023 1.335 27.056 -2.749 1.332 3.247 2.847 -4.313 27.162 2 AA_DG2DT3:DA10U7B11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DT 3 1_555 B DA 4 1_555 A DA 4 1_555 B DT 3 1_555 -0.433 -0.720 3.495 -0.017 9.026 43.108 -1.854 0.576 3.287 12.126 0.022 43.999 3 AA_DT3DA4:DT9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DA 4 1_555 B DT 3 1_555 A U7B 5 1_555 B DG 2 1_555 0.490 -1.687 3.742 -0.962 -3.218 30.108 -2.470 -1.165 3.880 -6.171 1.846 30.290 4 AA_DA4U7B5:DG8DT9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A U7B 5 1_555 B DG 2 1_555 A DG 6 1_555 B DC 1 1_555 -1.003 -0.219 3.262 1.766 11.043 30.384 -2.308 2.107 2.944 20.229 -3.234 32.331 5 AA_U7B5DG6:DC7DG8_BB A 5 ? B 8 ? A 6 ? B 7 ? # loop_ _pdbx_audit_support.funding_organization _pdbx_audit_support.country _pdbx_audit_support.grant_number _pdbx_audit_support.ordinal 'Spanish Ministry of Science, Innovation, and Universities' Spain BFU2017-89707-P 1 'Spanish Ministry of Science, Innovation, and Universities' Spain PRE2018-083173 2 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id U7B _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id U7B _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model AVANCE _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 7NBK _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 1.000000 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C F H N O P # loop_