data_8QE4 # _entry.id 8QE4 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.395 _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 8QE4 pdb_00008qe4 10.2210/pdb8qe4/pdb WWPDB D_1292133068 ? ? BMRB 34858 ? 10.13018/BMR34858 # 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 2024-06-26 2 'Structure model' 1 1 2024-07-31 # _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 ? # _pdbx_audit_revision_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group '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' citation 2 2 'Structure model' citation_author # 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' '_citation.journal_volume' 2 2 'Structure model' '_citation.page_first' 3 2 'Structure model' '_citation.page_last' 4 2 'Structure model' '_citation_author.identifier_ORCID' # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr . _pdbx_database_status.entry_id 8QE4 _pdbx_database_status.recvd_initial_deposition_date 2023-08-30 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs . _pdbx_database_status.status_code_nmr_data REL _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 . 8QDU unspecified BMRB ;Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions ; 34858 unspecified # _pdbx_contact_author.id 2 _pdbx_contact_author.email cgonzlaez@iqf.csic.es _pdbx_contact_author.name_first Carlos _pdbx_contact_author.name_last Gonzalez _pdbx_contact_author.name_mi ? _pdbx_contact_author.role 'principal investigator/group leader' _pdbx_contact_author.identifier_ORCID 0000-0001-8796-1282 # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'El-Khoury, R.' 1 ? 'Cabrero, C.' 2 ? 'Movilla, S.' 3 ? 'Friedland, D.' 4 ? 'Thorpe, J.D.' 5 ? 'Roman, M.' 6 ? 'Orozco, M.' 7 ? 'Gonzalez, C.' 8 ? 'Damha, M.' 9 ? # _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 UK _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_id_ASTM NARHAD _citation.journal_id_CSD 0389 _citation.journal_id_ISSN 1362-4962 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 52 _citation.language ? _citation.page_first 7414 _citation.page_last 7428 _citation.title ;Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions. ; _citation.year 2024 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1093/nar/gkae508 _citation.pdbx_database_id_PubMed 38874502 _citation.pdbx_database_id_patent ? _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'El-Khoury, R.' 1 ? primary 'Cabrero, C.' 2 ? primary 'Movilla, S.' 3 ? primary 'Kaur, H.' 4 ? primary 'Friedland, D.' 5 ? primary 'Dominguez, A.' 6 ? primary 'Thorpe, J.D.' 7 ? primary 'Roman, M.' 8 ? primary 'Orozco, M.' 9 ? primary 'Gonzalez, C.' 10 ? primary 'Damha, M.J.' 11 ? # _entity.id 1 _entity.type polymer _entity.src_method syn _entity.pdbx_description ;DNA (5'-D(*CP*(FRG)P*CP*(FRG)P*CP*(FRG))-3') ; _entity.formula_weight 1864.178 _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)(GF2)(DC)(GF2)(DC)(GF2)' _entity_poly.pdbx_seq_one_letter_code_can CXCXCX _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 GF2 n 1 3 DC n 1 4 GF2 n 1 5 DC n 1 6 GF2 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 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 GF2 'DNA linking' n ;2'-deoxy-2'-fluoroguanosine 5'-(dihydrogen phosphate) ; ? 'C10 H13 F N5 O7 P' 365.212 # 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 GF2 2 2 2 GF2 FRG A . n A 1 3 DC 3 3 3 DC DC A . n A 1 4 GF2 4 4 4 GF2 FRG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 GF2 6 6 6 GF2 FRG A . n B 1 1 DC 1 7 7 DC DC B . n B 1 2 GF2 2 8 8 GF2 FRG B . n B 1 3 DC 3 9 9 DC DC B . n B 1 4 GF2 4 10 10 GF2 FRG B . n B 1 5 DC 5 11 11 DC DC B . n B 1 6 GF2 6 12 12 GF2 FRG 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 8QE4 _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 8QE4 _struct.title ;Formation of left-handed helices by C2'-fluorinated nucleic acids under physiological salt conditions ; _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 8QE4 _struct_keywords.text ;2'F-ANA, 2'F-RNA, Z-DNA, 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 8QE4 _struct_ref.pdbx_db_accession 8QE4 _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 8QE4 A 1 ? 6 ? 8QE4 1 ? 6 ? 1 6 2 1 8QE4 B 1 ? 6 ? 8QE4 7 ? 12 ? 7 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 'NMR Distance Restraints' _pdbx_struct_assembly_auth_evidence.details 'not applicable' # _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 DC 1 "O3'" ? ? ? 1_555 A GF2 2 P ? ? A DC 1 A GF2 2 1_555 ? ? ? ? ? ? ? 1.614 ? ? covale2 covale one ? A GF2 2 "O3'" ? ? ? 1_555 A DC 3 P ? ? A GF2 2 A DC 3 1_555 ? ? ? ? ? ? ? 1.602 ? ? covale3 covale both ? A DC 3 "O3'" ? ? ? 1_555 A GF2 4 P ? ? A DC 3 A GF2 4 1_555 ? ? ? ? ? ? ? 1.600 ? ? covale4 covale one ? A GF2 4 "O3'" ? ? ? 1_555 A DC 5 P ? ? A GF2 4 A DC 5 1_555 ? ? ? ? ? ? ? 1.616 ? ? covale5 covale both ? A DC 5 "O3'" ? ? ? 1_555 A GF2 6 P ? ? A DC 5 A GF2 6 1_555 ? ? ? ? ? ? ? 1.615 ? ? covale6 covale both ? B DC 1 "O3'" ? ? ? 1_555 B GF2 2 P ? ? B DC 7 B GF2 8 1_555 ? ? ? ? ? ? ? 1.617 ? ? covale7 covale one ? B GF2 2 "O3'" ? ? ? 1_555 B DC 3 P ? ? B GF2 8 B DC 9 1_555 ? ? ? ? ? ? ? 1.606 ? ? covale8 covale both ? B DC 3 "O3'" ? ? ? 1_555 B GF2 4 P ? ? B DC 9 B GF2 10 1_555 ? ? ? ? ? ? ? 1.613 ? ? covale9 covale one ? B GF2 4 "O3'" ? ? ? 1_555 B DC 5 P ? ? B GF2 10 B DC 11 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale10 covale both ? B DC 5 "O3'" ? ? ? 1_555 B GF2 6 P ? ? B DC 11 B GF2 12 1_555 ? ? ? ? ? ? ? 1.611 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B GF2 6 N1 ? ? A DC 1 B GF2 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B GF2 6 O6 ? ? A DC 1 B GF2 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B GF2 6 N2 ? ? A DC 1 B GF2 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A GF2 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A GF2 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A GF2 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A GF2 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A GF2 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A GF2 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B GF2 4 N1 ? ? A DC 3 B GF2 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B GF2 4 O6 ? ? A DC 3 B GF2 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B GF2 4 N2 ? ? A DC 3 B GF2 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A GF2 4 N1 ? ? ? 1_555 B DC 3 N3 ? ? A GF2 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A GF2 4 N2 ? ? ? 1_555 B DC 3 O2 ? ? A GF2 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A GF2 4 O6 ? ? ? 1_555 B DC 3 N4 ? ? A GF2 4 B DC 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B GF2 2 N1 ? ? A DC 5 B GF2 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B GF2 2 O6 ? ? A DC 5 B GF2 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B GF2 2 N2 ? ? A DC 5 B GF2 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A GF2 6 N1 ? ? ? 1_555 B DC 1 N3 ? ? A GF2 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A GF2 6 N2 ? ? ? 1_555 B DC 1 O2 ? ? A GF2 6 B DC 7 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A GF2 6 O6 ? ? ? 1_555 B DC 1 N4 ? ? A GF2 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 ? ? "C2'" A DC 1 ? ? 100.59 105.90 -5.31 0.80 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.38 108.30 6.08 0.30 N 3 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 101.05 105.90 -4.85 0.80 N 4 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 115.00 108.30 6.70 0.30 N 5 1 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 114.98 108.30 6.68 0.30 N 6 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.72 105.90 -5.18 0.80 N 7 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.86 108.30 5.56 0.30 N 8 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 101.03 105.90 -4.87 0.80 N 9 1 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.10 108.30 5.80 0.30 N 10 1 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 97.67 102.20 -4.53 0.70 N 11 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 113.80 108.30 5.50 0.30 N 12 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.59 105.90 -5.31 0.80 N 13 2 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.66 108.30 6.36 0.30 N 14 2 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.24 108.30 5.94 0.30 N 15 2 N3 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 117.70 121.90 -4.20 0.70 N 16 2 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.78 102.20 -4.42 0.70 N 17 2 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.98 108.30 4.68 0.30 N 18 2 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.98 105.90 -4.92 0.80 N 19 2 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.41 108.30 5.11 0.30 N 20 2 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 99.99 105.90 -5.91 0.80 N 21 2 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.65 108.30 6.35 0.30 N 22 2 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 115.76 108.30 7.46 0.30 N 23 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 99.87 105.90 -6.03 0.80 N 24 3 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.86 108.30 6.56 0.30 N 25 3 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 100.36 105.90 -5.54 0.80 N 26 3 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.10 108.30 5.80 0.30 N 27 3 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 113.47 108.30 5.17 0.30 N 28 3 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.20 105.90 -5.70 0.80 N 29 3 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.84 108.30 5.54 0.30 N 30 3 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 100.51 105.90 -5.39 0.80 N 31 3 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.90 108.30 6.60 0.30 N 32 3 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.70 108.30 6.40 0.30 N 33 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 99.47 105.90 -6.43 0.80 N 34 4 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.95 108.30 6.65 0.30 N 35 4 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 113.97 108.30 5.67 0.30 N 36 4 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.99 102.20 -4.21 0.70 N 37 4 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.70 108.30 4.40 0.30 N 38 4 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 98.97 105.90 -6.93 0.80 N 39 4 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.55 108.30 5.25 0.30 N 40 4 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 98.65 105.90 -7.25 0.80 N 41 4 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.99 108.30 6.69 0.30 N 42 4 N3 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 117.61 121.90 -4.29 0.70 N 43 4 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 96.85 102.20 -5.35 0.70 N 44 4 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.80 108.30 6.50 0.30 N 45 5 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 99.74 105.90 -6.16 0.80 N 46 5 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.38 108.30 6.08 0.30 N 47 5 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 100.96 105.90 -4.94 0.80 N 48 5 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 115.20 108.30 6.90 0.30 N 49 5 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.85 108.30 3.55 0.30 N 50 5 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.38 105.90 -5.52 0.80 N 51 5 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 114.25 108.30 5.95 0.30 N 52 5 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 100.42 105.90 -5.48 0.80 N 53 5 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.20 108.30 5.90 0.30 N 54 5 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 97.86 102.20 -4.34 0.70 N 55 5 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 113.51 108.30 5.21 0.30 N 56 6 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.20 105.90 -5.70 0.80 N 57 6 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 115.44 108.30 7.14 0.30 N 58 6 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 99.61 105.90 -6.29 0.80 N 59 6 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.83 108.30 6.53 0.30 N 60 6 N1 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 122.58 118.90 3.68 0.60 N 61 6 N3 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 117.38 121.90 -4.52 0.70 N 62 6 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.05 102.20 -5.15 0.70 N 63 6 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.56 108.30 4.26 0.30 N 64 6 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.08 105.90 -5.82 0.80 N 65 6 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.53 108.30 5.23 0.30 N 66 6 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 99.06 105.90 -6.84 0.80 N 67 6 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.62 108.30 6.32 0.30 N 68 6 N3 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 117.44 121.90 -4.46 0.70 N 69 6 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 96.58 102.20 -5.62 0.70 N 70 6 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.31 108.30 6.01 0.30 N 71 7 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.26 105.90 -5.64 0.80 N 72 7 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 116.21 108.30 7.91 0.30 N 73 7 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 115.22 108.30 6.92 0.30 N 74 7 N3 A DC 3 ? ? C2 A DC 3 ? ? O2 A DC 3 ? ? 117.63 121.90 -4.27 0.70 N 75 7 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.79 102.20 -4.41 0.70 N 76 7 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.01 108.30 3.71 0.30 N 77 7 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? "C2'" B DC 7 ? ? 100.76 105.90 -5.14 0.80 N 78 7 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 113.40 108.30 5.10 0.30 N 79 7 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 100.91 105.90 -4.99 0.80 N 80 7 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.47 108.30 6.17 0.30 N 81 7 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 111.59 108.30 3.29 0.30 N 82 8 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 113.39 108.30 5.09 0.30 N 83 8 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 100.37 105.90 -5.53 0.80 N 84 8 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.60 108.30 6.30 0.30 N 85 8 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.91 102.20 -4.29 0.70 N 86 8 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.28 108.30 3.98 0.30 N 87 8 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 112.81 108.30 4.51 0.30 N 88 8 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 100.46 105.90 -5.44 0.80 N 89 8 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 114.95 108.30 6.65 0.30 N 90 8 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 97.48 102.20 -4.72 0.70 N 91 8 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.75 108.30 6.45 0.30 N 92 9 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 99.62 105.90 -6.28 0.80 N 93 9 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.48 108.30 6.18 0.30 N 94 9 N3 A DC 1 ? ? C2 A DC 1 ? ? O2 A DC 1 ? ? 117.60 121.90 -4.30 0.70 N 95 9 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? "C2'" A DC 3 ? ? 100.91 105.90 -4.99 0.80 N 96 9 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 114.58 108.30 6.28 0.30 N 97 9 "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? "C2'" A DC 5 ? ? 97.77 102.20 -4.43 0.70 N 98 9 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.03 108.30 3.73 0.30 N 99 9 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 112.13 108.30 3.83 0.30 N 100 9 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? "C2'" B DC 9 ? ? 100.06 105.90 -5.84 0.80 N 101 9 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 115.50 108.30 7.20 0.30 N 102 9 N3 B DC 9 ? ? C2 B DC 9 ? ? O2 B DC 9 ? ? 117.58 121.90 -4.32 0.70 N 103 9 "C4'" B DC 11 ? ? "C3'" B DC 11 ? ? "C2'" B DC 11 ? ? 97.36 102.20 -4.84 0.70 N 104 9 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.24 108.30 5.94 0.30 N 105 10 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? "C2'" A DC 1 ? ? 100.58 105.90 -5.32 0.80 N 106 10 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 114.22 108.30 5.92 0.30 N 107 10 N3 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 112.05 118.00 -5.95 0.70 N 108 10 C5 A DC 1 ? ? C4 A DC 1 ? ? N4 A DC 1 ? ? 124.79 120.20 4.59 0.70 N 109 10 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 113.41 108.30 5.11 0.30 N 110 10 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 112.41 108.30 4.11 0.30 N 111 10 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 112.33 108.30 4.03 0.30 N 112 10 N3 B DC 7 ? ? C4 B DC 7 ? ? N4 B DC 7 ? ? 113.71 118.00 -4.29 0.70 N 113 10 "O4'" B DC 9 ? ? "C1'" B DC 9 ? ? N1 B DC 9 ? ? 113.54 108.30 5.24 0.30 N 114 10 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 114.49 108.30 6.19 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 DC A 1 ? ? 0.082 'SIDE CHAIN' 2 1 DC A 5 ? ? 0.196 'SIDE CHAIN' 3 1 DC B 7 ? ? 0.090 'SIDE CHAIN' 4 1 DC B 11 ? ? 0.173 'SIDE CHAIN' 5 2 DC A 1 ? ? 0.097 'SIDE CHAIN' 6 2 DC A 5 ? ? 0.186 'SIDE CHAIN' 7 2 DC B 7 ? ? 0.104 'SIDE CHAIN' 8 2 DC B 11 ? ? 0.192 'SIDE CHAIN' 9 3 DC A 3 ? ? 0.062 'SIDE CHAIN' 10 3 DC A 5 ? ? 0.171 'SIDE CHAIN' 11 3 DC B 7 ? ? 0.083 'SIDE CHAIN' 12 3 DC B 11 ? ? 0.180 'SIDE CHAIN' 13 4 DC A 1 ? ? 0.106 'SIDE CHAIN' 14 4 DC A 5 ? ? 0.174 'SIDE CHAIN' 15 4 DC B 7 ? ? 0.070 'SIDE CHAIN' 16 4 DC B 11 ? ? 0.139 'SIDE CHAIN' 17 5 DC A 1 ? ? 0.076 'SIDE CHAIN' 18 5 DC A 5 ? ? 0.168 'SIDE CHAIN' 19 5 DC B 7 ? ? 0.061 'SIDE CHAIN' 20 5 DC B 11 ? ? 0.146 'SIDE CHAIN' 21 6 DC A 1 ? ? 0.063 'SIDE CHAIN' 22 6 DC A 5 ? ? 0.164 'SIDE CHAIN' 23 6 DC B 7 ? ? 0.083 'SIDE CHAIN' 24 6 DC B 11 ? ? 0.174 'SIDE CHAIN' 25 7 DC A 3 ? ? 0.063 'SIDE CHAIN' 26 7 DC A 5 ? ? 0.161 'SIDE CHAIN' 27 7 DC B 7 ? ? 0.107 'SIDE CHAIN' 28 7 DC B 11 ? ? 0.155 'SIDE CHAIN' 29 8 DC A 3 ? ? 0.069 'SIDE CHAIN' 30 8 DC A 5 ? ? 0.179 'SIDE CHAIN' 31 8 DC B 7 ? ? 0.129 'SIDE CHAIN' 32 8 DC B 11 ? ? 0.188 'SIDE CHAIN' 33 9 DC A 1 ? ? 0.060 'SIDE CHAIN' 34 9 DC A 3 ? ? 0.070 'SIDE CHAIN' 35 9 DC A 5 ? ? 0.158 'SIDE CHAIN' 36 9 DC B 7 ? ? 0.107 'SIDE CHAIN' 37 9 DC B 11 ? ? 0.170 'SIDE CHAIN' 38 10 DC A 1 ? ? 0.103 'SIDE CHAIN' 39 10 DC A 3 ? ? 0.061 'SIDE CHAIN' 40 10 DC A 5 ? ? 0.254 'SIDE CHAIN' 41 10 DC B 7 ? ? 0.173 'SIDE CHAIN' 42 10 DC B 11 ? ? 0.260 'SIDE CHAIN' # _pdbx_entry_details.entry_id 8QE4 _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest N _pdbx_entry_details.has_protein_modification ? # _pdbx_nmr_ensemble.entry_id 8QE4 _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 8QE4 _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'fewest violations' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents ;0.5 M DNA (5'-D(*CP*(FRG)P*CP*(FRG)P*CP*(FRG))-3'), 90% H2O/10% D2O ; _pdbx_nmr_sample_details.solvent_system '90% H2O/10% D2O' _pdbx_nmr_sample_details.label 'natural abundance' _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # _pdbx_nmr_exptl_sample.solution_id 1 _pdbx_nmr_exptl_sample.component ;DNA (5'-D(*CP*(FRG)P*CP*(FRG)P*CP*(FRG))-3') ; _pdbx_nmr_exptl_sample.concentration 0.5 _pdbx_nmr_exptl_sample.concentration_range ? _pdbx_nmr_exptl_sample.concentration_units M _pdbx_nmr_exptl_sample.isotopic_labeling 'natural abundance' # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 278 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 7 _pdbx_nmr_exptl_sample_conditions.ionic_strength 10 _pdbx_nmr_exptl_sample_conditions.details ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_err ? _pdbx_nmr_exptl_sample_conditions.ionic_strength_units mM _pdbx_nmr_exptl_sample_conditions.label 1H _pdbx_nmr_exptl_sample_conditions.pH_err ? _pdbx_nmr_exptl_sample_conditions.pH_units pH _pdbx_nmr_exptl_sample_conditions.pressure_err ? _pdbx_nmr_exptl_sample_conditions.temperature_err ? _pdbx_nmr_exptl_sample_conditions.temperature_units 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 1 1 '2D 1H-1H COSY' 1 isotropic # _pdbx_nmr_refine.entry_id 8QE4 _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 ? 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' 5 refinement Amber ? '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 DC OP3 O N N 1 DC P P N N 2 DC OP1 O N N 3 DC OP2 O N N 4 DC "O5'" O N N 5 DC "C5'" C N N 6 DC "C4'" C N R 7 DC "O4'" O N N 8 DC "C3'" C N S 9 DC "O3'" O N N 10 DC "C2'" C N N 11 DC "C1'" C N R 12 DC N1 N N N 13 DC C2 C N N 14 DC O2 O N N 15 DC N3 N N N 16 DC C4 C N N 17 DC N4 N N N 18 DC C5 C N N 19 DC C6 C N N 20 DC HOP3 H N N 21 DC HOP2 H N N 22 DC "H5'" H N N 23 DC "H5''" H N N 24 DC "H4'" H N N 25 DC "H3'" H N N 26 DC "HO3'" H N N 27 DC "H2'" H N N 28 DC "H2''" H N N 29 DC "H1'" H N N 30 DC H41 H N N 31 DC H42 H N N 32 DC H5 H N N 33 DC H6 H N N 34 GF2 F F N N 35 GF2 P P N N 36 GF2 N1 N N N 37 GF2 C2 C N N 38 GF2 N2 N N N 39 GF2 N3 N N N 40 GF2 C4 C Y N 41 GF2 C5 C Y N 42 GF2 C6 C N N 43 GF2 O6 O N N 44 GF2 N7 N Y N 45 GF2 C8 C Y N 46 GF2 N9 N Y N 47 GF2 "C1'" C N R 48 GF2 OP2 O N N 49 GF2 "C2'" C N R 50 GF2 OP1 O N N 51 GF2 "C3'" C N R 52 GF2 "O3'" O N N 53 GF2 "C4'" C N R 54 GF2 "O4'" O N N 55 GF2 "C5'" C N N 56 GF2 "O5'" O N N 57 GF2 OP3 O N N 58 GF2 HN1 H N N 59 GF2 HN2 H N N 60 GF2 HN2A H N N 61 GF2 H8 H N N 62 GF2 "H1'" H N N 63 GF2 HOP2 H N N 64 GF2 "H2'" H N N 65 GF2 "H3'" H N N 66 GF2 "HO3'" H N N 67 GF2 "H4'" H N N 68 GF2 "H5'" H N N 69 GF2 "H5'A" H N N 70 GF2 HOP3 H N N 71 # 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 DC OP3 P sing N N 1 DC OP3 HOP3 sing N N 2 DC P OP1 doub N N 3 DC P OP2 sing N N 4 DC P "O5'" sing N N 5 DC OP2 HOP2 sing N N 6 DC "O5'" "C5'" sing N N 7 DC "C5'" "C4'" sing N N 8 DC "C5'" "H5'" sing N N 9 DC "C5'" "H5''" sing N N 10 DC "C4'" "O4'" sing N N 11 DC "C4'" "C3'" sing N N 12 DC "C4'" "H4'" sing N N 13 DC "O4'" "C1'" sing N N 14 DC "C3'" "O3'" sing N N 15 DC "C3'" "C2'" sing N N 16 DC "C3'" "H3'" sing N N 17 DC "O3'" "HO3'" sing N N 18 DC "C2'" "C1'" sing N N 19 DC "C2'" "H2'" sing N N 20 DC "C2'" "H2''" sing N N 21 DC "C1'" N1 sing N N 22 DC "C1'" "H1'" sing N N 23 DC N1 C2 sing N N 24 DC N1 C6 sing N N 25 DC C2 O2 doub N N 26 DC C2 N3 sing N N 27 DC N3 C4 doub N N 28 DC C4 N4 sing N N 29 DC C4 C5 sing N N 30 DC N4 H41 sing N N 31 DC N4 H42 sing N N 32 DC C5 C6 doub N N 33 DC C5 H5 sing N N 34 DC C6 H6 sing N N 35 GF2 P "O5'" sing N N 36 GF2 N1 C2 sing N N 37 GF2 C2 N3 doub N N 38 GF2 C2 N2 sing N N 39 GF2 C4 N3 sing N N 40 GF2 C5 C4 doub Y N 41 GF2 C6 N1 sing N N 42 GF2 C6 C5 sing N N 43 GF2 O6 C6 doub N N 44 GF2 N7 C5 sing Y N 45 GF2 N7 C8 doub Y N 46 GF2 C8 N9 sing Y N 47 GF2 N9 C4 sing Y N 48 GF2 N9 "C1'" sing N N 49 GF2 "C1'" "O4'" sing N N 50 GF2 OP2 P sing N N 51 GF2 "C2'" F sing N N 52 GF2 "C2'" "C1'" sing N N 53 GF2 OP1 P doub N N 54 GF2 "C3'" "C2'" sing N N 55 GF2 "C3'" "C4'" sing N N 56 GF2 "O3'" "C3'" sing N N 57 GF2 "C4'" "O4'" sing N N 58 GF2 "C5'" "C4'" sing N N 59 GF2 "O5'" "C5'" sing N N 60 GF2 P OP3 sing N N 61 GF2 N1 HN1 sing N N 62 GF2 N2 HN2 sing N N 63 GF2 N2 HN2A sing N N 64 GF2 C8 H8 sing N N 65 GF2 "C1'" "H1'" sing N N 66 GF2 OP2 HOP2 sing N N 67 GF2 "C2'" "H2'" sing N N 68 GF2 "C3'" "H3'" sing N N 69 GF2 "O3'" "HO3'" sing N N 70 GF2 "C4'" "H4'" sing N N 71 GF2 "C5'" "H5'" sing N N 72 GF2 "C5'" "H5'A" sing N N 73 GF2 OP3 HOP3 sing N N 74 # _ndb_struct_conf_na.entry_id 8QE4 _ndb_struct_conf_na.feature 'z-form 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 GF2 6 1_555 0.060 -0.046 -0.170 29.695 14.671 -0.250 1 A_DC1:GF212_B A 1 ? B 12 ? 19 1 1 A GF2 2 1_555 B DC 5 1_555 -0.490 -0.160 -0.487 1.022 -0.449 -1.801 2 A_GF22:DC11_B A 2 ? B 11 ? 19 1 1 A DC 3 1_555 B GF2 4 1_555 0.203 -0.160 -0.305 -11.884 2.496 -0.051 3 A_DC3:GF210_B A 3 ? B 10 ? 19 1 1 A GF2 4 1_555 B DC 3 1_555 -0.098 -0.166 -0.318 10.707 5.621 -1.403 4 A_GF24:DC9_B A 4 ? B 9 ? 19 1 1 A DC 5 1_555 B GF2 2 1_555 0.354 -0.144 -0.268 -9.558 3.382 -1.714 5 A_DC5:GF28_B A 5 ? B 8 ? 19 1 1 A GF2 6 1_555 B DC 1 1_555 0.058 -0.078 -0.147 -27.780 22.980 -0.012 6 A_GF26: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 GF2 6 1_555 A GF2 2 1_555 B DC 5 1_555 0.588 4.935 3.819 12.166 -8.647 -14.553 -8.149 9.376 4.374 26.629 37.465 -20.818 1 AA_DC1GF22:DC11GF212_BB A 1 ? B 12 ? A 2 ? B 11 ? 1 A GF2 2 1_555 B DC 5 1_555 A DC 3 1_555 B GF2 4 1_555 -0.480 -2.596 3.343 -0.249 -21.386 -38.981 5.111 -0.657 1.753 29.507 -0.344 -44.262 2 AA_GF22DC3:GF210DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 1 A DC 3 1_555 B GF2 4 1_555 A GF2 4 1_555 B DC 3 1_555 -0.068 5.484 2.279 0.643 -1.710 -22.049 -13.796 0.008 2.692 4.461 1.679 -22.124 3 AA_DC3GF24:DC9GF210_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A GF2 4 1_555 B DC 3 1_555 A DC 5 1_555 B GF2 2 1_555 0.622 -2.258 3.606 -0.196 -18.399 -44.882 4.163 0.745 2.550 22.990 -0.245 -48.327 4 AA_GF24DC5:GF28DC9_BB A 4 ? B 9 ? A 5 ? B 8 ? 1 A DC 5 1_555 B GF2 2 1_555 A GF2 6 1_555 B DC 1 1_555 -0.474 4.585 3.587 -11.250 -3.445 -15.156 -11.682 -8.241 3.385 11.127 -36.336 -19.166 5 AA_DC5GF26:DC7GF28_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_nmr_spectrometer.spectrometer_id 1 _pdbx_nmr_spectrometer.model 'Neo AVANCE' _pdbx_nmr_spectrometer.type ? _pdbx_nmr_spectrometer.manufacturer Bruker _pdbx_nmr_spectrometer.field_strength 600 _pdbx_nmr_spectrometer.details ? # _atom_sites.entry_id 8QE4 _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.Cartn_transform_axes ? _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_