data_7D0Y # _entry.id 7D0Y # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.391 _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 7D0Y pdb_00007d0y 10.2210/pdb7d0y/pdb WWPDB D_1300015736 ? ? BMRB 36379 ? 10.13018/BMR36379 # 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 2021-02-03 2 'Structure model' 1 1 2021-02-10 3 'Structure model' 1 2 2021-04-28 4 'Structure model' 1 3 2024-05-01 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 4 'Structure model' 'Data collection' 4 4 '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' citation 2 2 'Structure model' citation_author 3 3 'Structure model' citation 4 3 'Structure model' citation_author 5 4 'Structure model' chem_comp_atom 6 4 'Structure model' chem_comp_bond 7 4 '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' '_citation.pdbx_database_id_PubMed' 2 2 'Structure model' '_citation.title' 3 2 'Structure model' '_citation_author.identifier_ORCID' 4 3 'Structure model' '_citation.journal_volume' 5 3 'Structure model' '_citation.page_first' 6 3 'Structure model' '_citation.page_last' 7 3 'Structure model' '_citation.title' 8 3 'Structure model' '_citation_author.identifier_ORCID' 9 4 'Structure model' '_database_2.pdbx_DOI' 10 4 '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 7D0Y _pdbx_database_status.recvd_initial_deposition_date 2020-09-12 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _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 # _pdbx_database_related.db_name BMRB _pdbx_database_related.details 'NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5' _pdbx_database_related.db_id 36379 _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Wan, L.' 1 0000-0003-3663-2678 'Guo, P.' 2 0000-0001-7760-5786 'Lam, S.L.' 3 0000-0001-5368-706X # _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 27 _citation.language ? _citation.page_first 6740 _citation.page_last 6747 _citation.title '5-Methylcytosine Substantially Enhances the Thermal Stability of DNA Minidumbbells.' _citation.year 2021 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1002/chem.202005410 _citation.pdbx_database_id_PubMed 33501691 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wan, L.' 1 0000-0003-3663-2678 primary 'Yi, J.' 2 ? primary 'Lam, S.L.' 3 0000-0001-5368-706X primary 'Lee, H.K.' 4 0000-0002-2052-4069 primary 'Guo, P.' 5 0000-0001-7760-5786 # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer syn ;DNA (5'-D(*(DCZ)P*(5CM)P*TP*GP*CP*(5CM)P*TP*G)-3') ; 2326.641 1 ? ? ? ? 2 non-polymer syn 'SODIUM ION' 22.990 5 ? ? ? ? # _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 '(DCZ)(5CM)(DT)(DG)(DC)(5CM)(DT)(DG)' _entity_poly.pdbx_seq_one_letter_code_can XCTGCCTG _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name 'SODIUM ION' _pdbx_entity_nonpoly.comp_id NA # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 DCZ n 1 2 5CM n 1 3 DT n 1 4 DG n 1 5 DC n 1 6 5CM n 1 7 DT n 1 8 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 8 _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _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 5CM 'DNA linking' n "5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE" ? 'C10 H16 N3 O7 P' 321.224 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DCZ 'DNA OH 5 prime terminus' . "2'-DEOXYCYTIDINE" ? 'C9 H13 N3 O4' 227.217 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 NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990 # 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 DCZ 1 1 1 DCZ CP5 A . n A 1 2 5CM 2 2 2 5CM MCP A . n A 1 3 DT 3 3 3 DT DT A . n A 1 4 DG 4 4 4 DG DG A . n A 1 5 DC 5 5 5 DC DC A . n A 1 6 5CM 6 6 6 5CM DMC A . n A 1 7 DT 7 7 7 DT DT A . n A 1 8 DG 8 8 8 DG DG A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NA 1 101 9 NA NA A . C 2 NA 1 102 10 NA NA A . D 2 NA 1 103 11 NA NA A . E 2 NA 1 104 12 NA NA A . F 2 NA 1 105 13 NA NA A . # _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 7D0Y _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 7D0Y _struct.title 'NMR solution structures of the DNA minidumbbell formed by two CmCTG repeats at pH 5' _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 7D0Y _struct_keywords.text 'minidumbbell, DNA, methylation, CCTG, 5-methylcytosine, pH 5' _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 2 ? C N N 2 ? D N N 2 ? E N N 2 ? F N N 2 ? # _struct_ref.id 1 _struct_ref.db_name PDB _struct_ref.db_code 7D0Y _struct_ref.pdbx_db_accession 7D0Y _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin 1 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 7D0Y _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 8 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession 7D0Y _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 8 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 8 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # 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)' 2080 ? 1 MORE -45 ? 1 'SSA (A^2)' 1100 ? # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # _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 one ? A DCZ 1 "O3'" ? ? ? 1_555 A 5CM 2 P ? ? A DCZ 1 A 5CM 2 1_555 ? ? ? ? ? ? ? 1.608 ? ? covale2 covale both ? A 5CM 2 "O3'" ? ? ? 1_555 A DT 3 P ? ? A 5CM 2 A DT 3 1_555 ? ? ? ? ? ? ? 1.605 ? ? covale3 covale both ? A DC 5 "O3'" ? ? ? 1_555 A 5CM 6 P ? ? A DC 5 A 5CM 6 1_555 ? ? ? ? ? ? ? 1.593 ? ? covale4 covale both ? A 5CM 6 "O3'" ? ? ? 1_555 A DT 7 P ? ? A 5CM 6 A DT 7 1_555 ? ? ? ? ? ? ? 1.606 ? ? metalc1 metalc ? ? A 5CM 2 OP2 ? ? ? 1_555 D NA . NA ? ? A 5CM 2 A NA 103 1_555 ? ? ? ? ? ? ? 2.246 ? ? metalc2 metalc ? ? A DT 3 OP2 ? ? ? 1_555 D NA . NA ? ? A DT 3 A NA 103 1_555 ? ? ? ? ? ? ? 2.230 ? ? metalc3 metalc ? ? A DT 3 OP1 ? ? ? 1_555 F NA . NA ? ? A DT 3 A NA 105 1_555 ? ? ? ? ? ? ? 2.207 ? ? metalc4 metalc ? ? A DG 4 OP2 ? ? ? 1_555 B NA . NA ? ? A DG 4 A NA 101 1_555 ? ? ? ? ? ? ? 2.249 ? ? metalc5 metalc ? ? A DG 4 "O5'" ? ? ? 1_555 B NA . NA ? ? A DG 4 A NA 101 1_555 ? ? ? ? ? ? ? 3.020 ? ? metalc6 metalc ? ? A DG 4 OP1 ? ? ? 1_555 F NA . NA ? ? A DG 4 A NA 105 1_555 ? ? ? ? ? ? ? 2.203 ? ? metalc7 metalc ? ? A DC 5 OP2 ? ? ? 1_555 B NA . NA ? ? A DC 5 A NA 101 1_555 ? ? ? ? ? ? ? 2.234 ? ? metalc8 metalc ? ? A DC 5 OP1 ? ? ? 1_555 E NA . NA ? ? A DC 5 A NA 104 1_555 ? ? ? ? ? ? ? 2.239 ? ? metalc9 metalc ? ? A DC 5 "O3'" ? ? ? 1_555 E NA . NA ? ? A DC 5 A NA 104 1_555 ? ? ? ? ? ? ? 2.435 ? ? metalc10 metalc ? ? A 5CM 6 OP1 ? ? ? 1_555 E NA . NA ? ? A 5CM 6 A NA 104 1_555 ? ? ? ? ? ? ? 2.282 ? ? metalc11 metalc ? ? A DT 7 OP1 ? ? ? 1_555 C NA . NA ? ? A DT 7 A NA 102 1_555 ? ? ? ? ? ? ? 2.191 ? ? metalc12 metalc ? ? A DG 8 OP1 ? ? ? 1_555 C NA . NA ? ? A DG 8 A NA 102 1_555 ? ? ? ? ? ? ? 2.189 ? ? hydrog1 hydrog ? ? A 5CM 2 N4 ? ? ? 1_555 A 5CM 6 O2 ? ? A 5CM 2 A 5CM 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog2 hydrog ? ? A 5CM 2 O2 ? ? ? 1_555 A 5CM 6 N4 ? ? A 5CM 2 A 5CM 6 1_555 ? ? ? ? ? ? TYPE_15_PAIR ? ? ? hydrog3 hydrog ? ? A DC 5 N3 ? ? ? 1_555 A DG 8 N1 ? ? A DC 5 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DC 5 N4 ? ? ? 1_555 A DG 8 O6 ? ? A DC 5 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DC 5 O2 ? ? ? 1_555 A DG 8 N2 ? ? A DC 5 A DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference covale ? ? metalc ? ? hydrog ? ? # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 OP2 ? A 5CM 2 ? A 5CM 2 ? 1_555 NA ? D NA . ? A NA 103 ? 1_555 OP2 ? A DT 3 ? A DT 3 ? 1_555 121.3 ? 2 OP1 ? A DT 3 ? A DT 3 ? 1_555 NA ? F NA . ? A NA 105 ? 1_555 OP1 ? A DG 4 ? A DG 4 ? 1_555 124.2 ? 3 OP2 ? A DG 4 ? A DG 4 ? 1_555 NA ? B NA . ? A NA 101 ? 1_555 "O5'" ? A DG 4 ? A DG 4 ? 1_555 52.4 ? 4 OP2 ? A DG 4 ? A DG 4 ? 1_555 NA ? B NA . ? A NA 101 ? 1_555 OP2 ? A DC 5 ? A DC 5 ? 1_555 141.5 ? 5 "O5'" ? A DG 4 ? A DG 4 ? 1_555 NA ? B NA . ? A NA 101 ? 1_555 OP2 ? A DC 5 ? A DC 5 ? 1_555 95.6 ? 6 OP1 ? A DC 5 ? A DC 5 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 "O3'" ? A DC 5 ? A DC 5 ? 1_555 109.4 ? 7 OP1 ? A DC 5 ? A DC 5 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 OP1 ? A 5CM 6 ? A 5CM 6 ? 1_555 170.1 ? 8 "O3'" ? A DC 5 ? A DC 5 ? 1_555 NA ? E NA . ? A NA 104 ? 1_555 OP1 ? A 5CM 6 ? A 5CM 6 ? 1_555 60.8 ? 9 OP1 ? A DT 7 ? A DT 7 ? 1_555 NA ? C NA . ? A NA 102 ? 1_555 OP1 ? A DG 8 ? A DG 8 ? 1_555 116.8 ? # 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 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.65 122.90 -4.25 0.60 N 2 1 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.56 108.30 3.26 0.30 N 3 1 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 110.46 108.30 2.16 0.30 N 4 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.23 122.90 -3.67 0.60 N 5 1 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.46 108.30 2.16 0.30 N 6 2 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.03 122.90 -3.87 0.60 N 7 2 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.97 108.30 3.67 0.30 N 8 2 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 111.52 108.30 3.22 0.30 N 9 2 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 117.70 121.90 -4.20 0.70 N 10 2 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.26 122.90 -3.64 0.60 N 11 2 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.83 108.30 2.53 0.30 N 12 3 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.24 122.90 -3.66 0.60 N 13 3 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.18 108.30 3.88 0.30 N 14 3 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 110.57 108.30 2.27 0.30 N 15 3 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.11 122.90 -3.79 0.60 N 16 3 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.75 108.30 2.45 0.30 N 17 4 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.93 122.90 -3.97 0.60 N 18 4 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.46 108.30 3.16 0.30 N 19 4 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 104.02 110.10 -6.08 1.00 N 20 4 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 110.68 108.30 2.38 0.30 N 21 4 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.17 122.90 -3.73 0.60 N 22 4 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.57 108.30 2.27 0.30 N 23 5 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.27 122.90 -3.63 0.60 N 24 5 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.27 108.30 3.97 0.30 N 25 5 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.60 128.60 -3.00 0.50 N 26 5 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 111.24 108.30 2.94 0.30 N 27 5 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.17 122.90 -3.73 0.60 N 28 5 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.73 108.30 2.43 0.30 N 29 6 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.74 122.90 -4.16 0.60 N 30 6 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.40 108.30 4.10 0.30 N 31 6 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.20 122.90 -3.70 0.60 N 32 6 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 112.98 108.30 4.68 0.30 N 33 7 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.69 122.90 -4.21 0.60 N 34 7 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.63 108.30 3.33 0.30 N 35 7 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 111.00 108.30 2.70 0.30 N 36 7 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.22 122.90 -3.68 0.60 N 37 7 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.81 108.30 2.51 0.30 N 38 8 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.28 122.90 -3.62 0.60 N 39 8 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.39 108.30 4.09 0.30 N 40 8 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 111.24 108.30 2.94 0.30 N 41 8 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.06 122.90 -3.84 0.60 N 42 8 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.52 108.30 2.22 0.30 N 43 9 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.95 122.90 -3.95 0.60 N 44 9 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.79 108.30 3.49 0.30 N 45 9 "C3'" A DC 5 ? ? "O3'" A DC 5 ? ? P A 5CM 6 ? ? 127.68 119.70 7.98 1.20 Y 46 9 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.10 122.90 -3.80 0.60 N 47 9 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.94 108.30 3.64 0.30 N 48 10 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.24 122.90 -3.66 0.60 N 49 10 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.84 108.30 4.54 0.30 N 50 10 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.12 128.60 -3.48 0.50 N 51 10 "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? "C3'" A DC 5 ? ? 102.01 104.50 -2.49 0.40 N 52 10 "C3'" A DC 5 ? ? "O3'" A DC 5 ? ? P A 5CM 6 ? ? 126.91 119.70 7.21 1.20 Y 53 10 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.15 122.90 -3.75 0.60 N 54 10 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.75 108.30 2.45 0.30 N 55 11 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.12 122.90 -3.78 0.60 N 56 11 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.84 108.30 3.54 0.30 N 57 11 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.73 110.10 -6.37 1.00 N 58 11 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.62 108.30 2.32 0.30 N 59 11 "C3'" A 5CM 6 ? ? "O3'" A 5CM 6 ? ? P A DT 7 ? ? 127.12 119.70 7.42 1.20 Y 60 11 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.28 122.90 -3.62 0.60 N 61 11 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.70 108.30 2.40 0.30 N 62 12 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.21 122.90 -3.69 0.60 N 63 12 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.07 108.30 3.77 0.30 N 64 12 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.54 128.60 -3.06 0.50 N 65 12 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.22 122.90 -3.68 0.60 N 66 12 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.49 108.30 3.19 0.30 N 67 13 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.57 122.90 -4.33 0.60 N 68 13 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.94 108.30 3.64 0.30 N 69 13 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.21 128.60 -3.39 0.50 N 70 13 N1 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 122.74 118.90 3.84 0.60 N 71 13 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 117.51 121.90 -4.39 0.70 N 72 13 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.30 122.90 -3.60 0.60 N 73 13 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.66 108.30 2.36 0.30 N 74 14 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.81 122.90 -4.09 0.60 N 75 14 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.50 108.30 4.20 0.30 N 76 14 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.36 108.30 2.06 0.30 N 77 14 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.07 122.90 -3.83 0.60 N 78 14 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 112.69 108.30 4.39 0.30 N 79 15 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.61 122.90 -4.29 0.60 N 80 15 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.18 108.30 3.88 0.30 N 81 15 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.25 128.60 -3.35 0.50 N 82 15 N1 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 122.59 118.90 3.69 0.60 N 83 15 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 117.48 121.90 -4.42 0.70 N 84 16 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.87 122.90 -4.03 0.60 N 85 16 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.67 108.30 4.37 0.30 N 86 16 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.08 122.90 -3.82 0.60 N 87 16 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.52 108.30 2.22 0.30 N 88 17 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.15 122.90 -3.75 0.60 N 89 17 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.56 108.30 3.26 0.30 N 90 17 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.97 110.10 -6.13 1.00 N 91 17 "C3'" A 5CM 6 ? ? "O3'" A 5CM 6 ? ? P A DT 7 ? ? 127.07 119.70 7.37 1.20 Y 92 17 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.25 122.90 -3.65 0.60 N 93 17 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.68 108.30 2.38 0.30 N 94 18 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.08 122.90 -3.82 0.60 N 95 18 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 112.13 108.30 3.83 0.30 N 96 18 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.79 110.10 -6.31 1.00 N 97 18 "O4'" A DC 5 ? ? "C1'" A DC 5 ? ? N1 A DC 5 ? ? 110.61 108.30 2.31 0.30 N 98 18 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.20 122.90 -3.70 0.60 N 99 18 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 111.36 108.30 3.06 0.30 N 100 19 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 118.89 122.90 -4.01 0.60 N 101 19 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.95 108.30 3.65 0.30 N 102 19 N3 A DG 4 ? ? C4 A DG 4 ? ? C5 A DG 4 ? ? 125.43 128.60 -3.17 0.50 N 103 19 N3 A DC 5 ? ? C2 A DC 5 ? ? O2 A DC 5 ? ? 117.68 121.90 -4.22 0.70 N 104 19 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.27 122.90 -3.63 0.60 N 105 19 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 110.50 108.30 2.20 0.30 N 106 20 C6 A DT 3 ? ? C5 A DT 3 ? ? C7 A DT 3 ? ? 119.27 122.90 -3.63 0.60 N 107 20 "O4'" A DG 4 ? ? "C1'" A DG 4 ? ? N9 A DG 4 ? ? 111.64 108.30 3.34 0.30 N 108 20 "C1'" A DC 5 ? ? "O4'" A DC 5 ? ? "C4'" A DC 5 ? ? 103.60 110.10 -6.50 1.00 N 109 20 "O4'" A DT 7 ? ? "C1'" A DT 7 ? ? N1 A DT 7 ? ? 110.18 108.30 1.88 0.30 N 110 20 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 119.23 122.90 -3.67 0.60 N 111 20 "O4'" A DG 8 ? ? "C1'" A DG 8 ? ? N9 A DG 8 ? ? 112.81 108.30 4.51 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 5 ? ? 0.070 'SIDE CHAIN' 2 2 DT A 3 ? ? 0.070 'SIDE CHAIN' 3 2 DG A 4 ? ? 0.058 'SIDE CHAIN' 4 3 DC A 5 ? ? 0.074 'SIDE CHAIN' 5 5 DC A 5 ? ? 0.073 'SIDE CHAIN' 6 6 DG A 8 ? ? 0.073 'SIDE CHAIN' 7 7 DC A 5 ? ? 0.063 'SIDE CHAIN' 8 8 DC A 5 ? ? 0.059 'SIDE CHAIN' 9 9 DG A 8 ? ? 0.081 'SIDE CHAIN' 10 10 DG A 4 ? ? 0.089 'SIDE CHAIN' 11 10 DT A 7 ? ? 0.087 'SIDE CHAIN' 12 10 DG A 8 ? ? 0.064 'SIDE CHAIN' 13 11 DT A 3 ? ? 0.065 'SIDE CHAIN' 14 11 DG A 8 ? ? 0.059 'SIDE CHAIN' 15 12 DG A 4 ? ? 0.053 'SIDE CHAIN' 16 13 DT A 7 ? ? 0.094 'SIDE CHAIN' 17 13 DG A 8 ? ? 0.056 'SIDE CHAIN' 18 14 DG A 8 ? ? 0.077 'SIDE CHAIN' 19 15 DT A 7 ? ? 0.072 'SIDE CHAIN' 20 17 DC A 5 ? ? 0.068 'SIDE CHAIN' 21 18 DG A 8 ? ? 0.054 'SIDE CHAIN' 22 19 DT A 7 ? ? 0.067 'SIDE CHAIN' 23 19 DG A 8 ? ? 0.063 'SIDE CHAIN' 24 20 DG A 4 ? ? 0.058 'SIDE CHAIN' 25 20 DC A 5 ? ? 0.063 'SIDE CHAIN' 26 20 DG A 8 ? ? 0.069 'SIDE CHAIN' # _pdbx_entry_details.entry_id 7D0Y _pdbx_entry_details.has_ligand_of_interest Y _pdbx_entry_details.compound_details 'DCZ (A 1), 5CM (A 2) have extra atom H3 as N3-site protonated.' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? # _pdbx_nmr_ensemble.entry_id 7D0Y _pdbx_nmr_ensemble.conformers_calculated_total_number 500 _pdbx_nmr_ensemble.conformers_submitted_total_number 20 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _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 7D0Y _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # _pdbx_nmr_sample_details.solution_id 1 _pdbx_nmr_sample_details.contents '0.2 mM NA DNA, 0.02 mM NA DSS, 10 mM NA NaCl, 99.96% D2O' _pdbx_nmr_sample_details.solvent_system '99.96% D2O' _pdbx_nmr_sample_details.label 'CmCTG2, pH 5, D2O' _pdbx_nmr_sample_details.type solution _pdbx_nmr_sample_details.details ? # 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 0.2 ? mM NA 1 DSS 0.02 ? mM NA 1 NaCl 10 ? mM NA # _pdbx_nmr_exptl_sample_conditions.conditions_id 1 _pdbx_nmr_exptl_sample_conditions.temperature 273 _pdbx_nmr_exptl_sample_conditions.pressure_units atm _pdbx_nmr_exptl_sample_conditions.pressure 1 _pdbx_nmr_exptl_sample_conditions.pH 5 _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 'pH 5' _pdbx_nmr_exptl_sample_conditions.pH_err 0.1 _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 5 1 1 '2D 1H-1H COSY' 2 isotropic 6 1 1 '2D 1H-1H TOCSY' 2 isotropic # _pdbx_nmr_refine.entry_id 7D0Y _pdbx_nmr_refine.method 'restrained molecular dynamics' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 2 # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 'chemical shift assignment' TopSpin ? 'Bruker Biospin' 2 'structure calculation' Amber ? 'Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman' # 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 5CM N1 N N N 1 5CM C2 C N N 2 5CM N3 N N N 3 5CM C4 C N N 4 5CM C5 C N N 5 5CM C5A C N N 6 5CM C6 C N N 7 5CM O2 O N N 8 5CM N4 N N N 9 5CM "C1'" C N R 10 5CM "C2'" C N N 11 5CM "C3'" C N S 12 5CM "C4'" C N R 13 5CM "O4'" O N N 14 5CM "O3'" O N N 15 5CM "C5'" C N N 16 5CM "O5'" O N N 17 5CM P P N N 18 5CM OP1 O N N 19 5CM OP2 O N N 20 5CM OP3 O N N 21 5CM H5A1 H N N 22 5CM H5A2 H N N 23 5CM H5A3 H N N 24 5CM H6 H N N 25 5CM HN41 H N N 26 5CM HN42 H N N 27 5CM "H1'" H N N 28 5CM "H2'" H N N 29 5CM "H2''" H N N 30 5CM "H3'" H N N 31 5CM "H4'" H N N 32 5CM "HO3'" H N N 33 5CM "H5'" H N N 34 5CM "H5''" H N N 35 5CM HOP2 H N N 36 5CM HOP3 H N N 37 DC OP3 O N N 38 DC P P N N 39 DC OP1 O N N 40 DC OP2 O N N 41 DC "O5'" O N N 42 DC "C5'" C N N 43 DC "C4'" C N R 44 DC "O4'" O N N 45 DC "C3'" C N S 46 DC "O3'" O N N 47 DC "C2'" C N N 48 DC "C1'" C N R 49 DC N1 N N N 50 DC C2 C N N 51 DC O2 O N N 52 DC N3 N N N 53 DC C4 C N N 54 DC N4 N N N 55 DC C5 C N N 56 DC C6 C N N 57 DC HOP3 H N N 58 DC HOP2 H N N 59 DC "H5'" H N N 60 DC "H5''" H N N 61 DC "H4'" H N N 62 DC "H3'" H N N 63 DC "HO3'" H N N 64 DC "H2'" H N N 65 DC "H2''" H N N 66 DC "H1'" H N N 67 DC H41 H N N 68 DC H42 H N N 69 DC H5 H N N 70 DC H6 H N N 71 DCZ N1 N N N 72 DCZ C2 C N N 73 DCZ N3 N N N 74 DCZ C4 C N N 75 DCZ C5 C N N 76 DCZ C6 C N N 77 DCZ O2 O N N 78 DCZ N4 N N N 79 DCZ "C1'" C N R 80 DCZ "C2'" C N N 81 DCZ "C3'" C N S 82 DCZ "C4'" C N R 83 DCZ "O4'" O N N 84 DCZ "O3'" O N N 85 DCZ "C5'" C N N 86 DCZ "O5'" O N N 87 DCZ H5 H N N 88 DCZ H6 H N N 89 DCZ HN41 H N N 90 DCZ HN42 H N N 91 DCZ "H1'" H N N 92 DCZ "H2'1" H N N 93 DCZ "H2'2" H N N 94 DCZ "H3'" H N N 95 DCZ "H4'" H N N 96 DCZ "HO3'" H N N 97 DCZ "H5'1" H N N 98 DCZ "H5'2" H N N 99 DCZ HO51 H N N 100 DG OP3 O N N 101 DG P P N N 102 DG OP1 O N N 103 DG OP2 O N N 104 DG "O5'" O N N 105 DG "C5'" C N N 106 DG "C4'" C N R 107 DG "O4'" O N N 108 DG "C3'" C N S 109 DG "O3'" O N N 110 DG "C2'" C N N 111 DG "C1'" C N R 112 DG N9 N Y N 113 DG C8 C Y N 114 DG N7 N Y N 115 DG C5 C Y N 116 DG C6 C N N 117 DG O6 O N N 118 DG N1 N N N 119 DG C2 C N N 120 DG N2 N N N 121 DG N3 N N N 122 DG C4 C Y N 123 DG HOP3 H N N 124 DG HOP2 H N N 125 DG "H5'" H N N 126 DG "H5''" H N N 127 DG "H4'" H N N 128 DG "H3'" H N N 129 DG "HO3'" H N N 130 DG "H2'" H N N 131 DG "H2''" H N N 132 DG "H1'" H N N 133 DG H8 H N N 134 DG H1 H N N 135 DG H21 H N N 136 DG H22 H N N 137 DT OP3 O N N 138 DT P P N N 139 DT OP1 O N N 140 DT OP2 O N N 141 DT "O5'" O N N 142 DT "C5'" C N N 143 DT "C4'" C N R 144 DT "O4'" O N N 145 DT "C3'" C N S 146 DT "O3'" O N N 147 DT "C2'" C N N 148 DT "C1'" C N R 149 DT N1 N N N 150 DT C2 C N N 151 DT O2 O N N 152 DT N3 N N N 153 DT C4 C N N 154 DT O4 O N N 155 DT C5 C N N 156 DT C7 C N N 157 DT C6 C N N 158 DT HOP3 H N N 159 DT HOP2 H N N 160 DT "H5'" H N N 161 DT "H5''" H N N 162 DT "H4'" H N N 163 DT "H3'" H N N 164 DT "HO3'" H N N 165 DT "H2'" H N N 166 DT "H2''" H N N 167 DT "H1'" H N N 168 DT H3 H N N 169 DT H71 H N N 170 DT H72 H N N 171 DT H73 H N N 172 DT H6 H N N 173 NA NA NA N N 174 # 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 5CM N1 C2 sing N N 1 5CM N1 C6 sing N N 2 5CM N1 "C1'" sing N N 3 5CM C2 N3 sing N N 4 5CM C2 O2 doub N N 5 5CM N3 C4 doub N N 6 5CM C4 C5 sing N N 7 5CM C4 N4 sing N N 8 5CM C5 C5A sing N N 9 5CM C5 C6 doub N N 10 5CM C5A H5A1 sing N N 11 5CM C5A H5A2 sing N N 12 5CM C5A H5A3 sing N N 13 5CM C6 H6 sing N N 14 5CM N4 HN41 sing N N 15 5CM N4 HN42 sing N N 16 5CM "C1'" "C2'" sing N N 17 5CM "C1'" "O4'" sing N N 18 5CM "C1'" "H1'" sing N N 19 5CM "C2'" "C3'" sing N N 20 5CM "C2'" "H2'" sing N N 21 5CM "C2'" "H2''" sing N N 22 5CM "C3'" "C4'" sing N N 23 5CM "C3'" "O3'" sing N N 24 5CM "C3'" "H3'" sing N N 25 5CM "C4'" "O4'" sing N N 26 5CM "C4'" "C5'" sing N N 27 5CM "C4'" "H4'" sing N N 28 5CM "O3'" "HO3'" sing N N 29 5CM "C5'" "O5'" sing N N 30 5CM "C5'" "H5'" sing N N 31 5CM "C5'" "H5''" sing N N 32 5CM "O5'" P sing N N 33 5CM P OP1 doub N N 34 5CM P OP2 sing N N 35 5CM P OP3 sing N N 36 5CM OP2 HOP2 sing N N 37 5CM OP3 HOP3 sing N 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 DCZ N1 C2 sing N N 74 DCZ N1 C6 sing N N 75 DCZ N1 "C1'" sing N N 76 DCZ C2 N3 sing N N 77 DCZ C2 O2 doub N N 78 DCZ N3 C4 doub N N 79 DCZ C4 C5 sing N N 80 DCZ C4 N4 sing N N 81 DCZ C5 C6 doub N N 82 DCZ C5 H5 sing N N 83 DCZ C6 H6 sing N N 84 DCZ N4 HN41 sing N N 85 DCZ N4 HN42 sing N N 86 DCZ "C1'" "C2'" sing N N 87 DCZ "C1'" "O4'" sing N N 88 DCZ "C1'" "H1'" sing N N 89 DCZ "C2'" "C3'" sing N N 90 DCZ "C2'" "H2'1" sing N N 91 DCZ "C2'" "H2'2" sing N N 92 DCZ "C3'" "C4'" sing N N 93 DCZ "C3'" "O3'" sing N N 94 DCZ "C3'" "H3'" sing N N 95 DCZ "C4'" "O4'" sing N N 96 DCZ "C4'" "C5'" sing N N 97 DCZ "C4'" "H4'" sing N N 98 DCZ "O3'" "HO3'" sing N N 99 DCZ "C5'" "O5'" sing N N 100 DCZ "C5'" "H5'1" sing N N 101 DCZ "C5'" "H5'2" sing N N 102 DCZ "O5'" HO51 sing N N 103 DG OP3 P sing N N 104 DG OP3 HOP3 sing N N 105 DG P OP1 doub N N 106 DG P OP2 sing N N 107 DG P "O5'" sing N N 108 DG OP2 HOP2 sing N N 109 DG "O5'" "C5'" sing N N 110 DG "C5'" "C4'" sing N N 111 DG "C5'" "H5'" sing N N 112 DG "C5'" "H5''" sing N N 113 DG "C4'" "O4'" sing N N 114 DG "C4'" "C3'" sing N N 115 DG "C4'" "H4'" sing N N 116 DG "O4'" "C1'" sing N N 117 DG "C3'" "O3'" sing N N 118 DG "C3'" "C2'" sing N N 119 DG "C3'" "H3'" sing N N 120 DG "O3'" "HO3'" sing N N 121 DG "C2'" "C1'" sing N N 122 DG "C2'" "H2'" sing N N 123 DG "C2'" "H2''" sing N N 124 DG "C1'" N9 sing N N 125 DG "C1'" "H1'" sing N N 126 DG N9 C8 sing Y N 127 DG N9 C4 sing Y N 128 DG C8 N7 doub Y N 129 DG C8 H8 sing N N 130 DG N7 C5 sing Y N 131 DG C5 C6 sing N N 132 DG C5 C4 doub Y N 133 DG C6 O6 doub N N 134 DG C6 N1 sing N N 135 DG N1 C2 sing N N 136 DG N1 H1 sing N N 137 DG C2 N2 sing N N 138 DG C2 N3 doub N N 139 DG N2 H21 sing N N 140 DG N2 H22 sing N N 141 DG N3 C4 sing N N 142 DT OP3 P sing N N 143 DT OP3 HOP3 sing N N 144 DT P OP1 doub N N 145 DT P OP2 sing N N 146 DT P "O5'" sing N N 147 DT OP2 HOP2 sing N N 148 DT "O5'" "C5'" sing N N 149 DT "C5'" "C4'" sing N N 150 DT "C5'" "H5'" sing N N 151 DT "C5'" "H5''" sing N N 152 DT "C4'" "O4'" sing N N 153 DT "C4'" "C3'" sing N N 154 DT "C4'" "H4'" sing N N 155 DT "O4'" "C1'" sing N N 156 DT "C3'" "O3'" sing N N 157 DT "C3'" "C2'" sing N N 158 DT "C3'" "H3'" sing N N 159 DT "O3'" "HO3'" sing N N 160 DT "C2'" "C1'" sing N N 161 DT "C2'" "H2'" sing N N 162 DT "C2'" "H2''" sing N N 163 DT "C1'" N1 sing N N 164 DT "C1'" "H1'" sing N N 165 DT N1 C2 sing N N 166 DT N1 C6 sing N N 167 DT C2 O2 doub N N 168 DT C2 N3 sing N N 169 DT N3 C4 sing N N 170 DT N3 H3 sing N N 171 DT C4 O4 doub N N 172 DT C4 C5 sing N N 173 DT C5 C7 sing N N 174 DT C5 C6 doub N N 175 DT C7 H71 sing N N 176 DT C7 H72 sing N N 177 DT C7 H73 sing N N 178 DT C6 H6 sing N N 179 # _ndb_struct_conf_na.entry_id 7D0Y _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 5CM 2 1_555 A 5CM 6 1_555 2.060 1.751 0.246 -19.322 -8.599 179.456 1 A_5CM2:5CM6_A A 2 ? A 6 ? 15 2 1 A DG 8 1_555 A DC 5 1_555 -0.424 -0.192 -0.032 -7.901 -0.158 -1.233 2 A_DG8:DC5_A A 8 ? A 5 ? 19 1 # _ndb_struct_na_base_pair_step.model_number 1 _ndb_struct_na_base_pair_step.i_label_asym_id_1 A _ndb_struct_na_base_pair_step.i_label_comp_id_1 5CM _ndb_struct_na_base_pair_step.i_label_seq_id_1 2 _ndb_struct_na_base_pair_step.i_symmetry_1 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_1 A _ndb_struct_na_base_pair_step.j_label_comp_id_1 5CM _ndb_struct_na_base_pair_step.j_label_seq_id_1 6 _ndb_struct_na_base_pair_step.j_symmetry_1 1_555 _ndb_struct_na_base_pair_step.i_label_asym_id_2 A _ndb_struct_na_base_pair_step.i_label_comp_id_2 DG _ndb_struct_na_base_pair_step.i_label_seq_id_2 8 _ndb_struct_na_base_pair_step.i_symmetry_2 1_555 _ndb_struct_na_base_pair_step.j_label_asym_id_2 A _ndb_struct_na_base_pair_step.j_label_comp_id_2 DC _ndb_struct_na_base_pair_step.j_label_seq_id_2 5 _ndb_struct_na_base_pair_step.j_symmetry_2 1_555 _ndb_struct_na_base_pair_step.shift 5.231 _ndb_struct_na_base_pair_step.slide 3.142 _ndb_struct_na_base_pair_step.rise 2.580 _ndb_struct_na_base_pair_step.tilt 29.641 _ndb_struct_na_base_pair_step.roll -76.301 _ndb_struct_na_base_pair_step.twist 62.430 _ndb_struct_na_base_pair_step.x_displacement 3.013 _ndb_struct_na_base_pair_step.y_displacement -3.057 _ndb_struct_na_base_pair_step.helical_rise 0.993 _ndb_struct_na_base_pair_step.inclination -55.120 _ndb_struct_na_base_pair_step.tip -21.413 _ndb_struct_na_base_pair_step.helical_twist 99.495 _ndb_struct_na_base_pair_step.step_number 1 _ndb_struct_na_base_pair_step.step_name AA_5CM2DG8:DC55CM6_AA _ndb_struct_na_base_pair_step.i_auth_asym_id_1 A _ndb_struct_na_base_pair_step.i_auth_seq_id_1 2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_1 A _ndb_struct_na_base_pair_step.j_auth_seq_id_1 6 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 ? _ndb_struct_na_base_pair_step.i_auth_asym_id_2 A _ndb_struct_na_base_pair_step.i_auth_seq_id_2 8 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 ? _ndb_struct_na_base_pair_step.j_auth_asym_id_2 A _ndb_struct_na_base_pair_step.j_auth_seq_id_2 5 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 ? # loop_ _pdbx_entity_instance_feature.ordinal _pdbx_entity_instance_feature.comp_id _pdbx_entity_instance_feature.asym_id _pdbx_entity_instance_feature.seq_num _pdbx_entity_instance_feature.auth_comp_id _pdbx_entity_instance_feature.auth_asym_id _pdbx_entity_instance_feature.auth_seq_num _pdbx_entity_instance_feature.feature_type _pdbx_entity_instance_feature.details 1 5CM ? ? 5CM ? ? 'SUBJECT OF INVESTIGATION' ? 2 5CM ? ? 5CM ? ? 'SUBJECT OF INVESTIGATION' ? # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 AVANCE ? Bruker 700 ? 2 AVANCE ? Bruker 500 ? # _atom_sites.entry_id 7D0Y _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 H N NA O P # loop_