data_1FD5 # _entry.id 1FD5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 1FD5 pdb_00001fd5 10.2210/pdb1fd5/pdb NDB DD0028 ? ? RCSB RCSB011493 ? ? WWPDB D_1000011493 ? ? # 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 2000-08-07 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2024-02-07 6 'Structure model' 1 5 2024-03-13 # _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' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Refinement description' 5 5 'Structure model' 'Data collection' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 6 'Structure model' 'Source and taxonomy' 9 6 'Structure model' 'Structure summary' # 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 4 'Structure model' software 2 5 'Structure model' chem_comp_atom 3 5 'Structure model' chem_comp_bond 4 5 'Structure model' database_2 5 5 'Structure model' pdbx_struct_conn_angle 6 5 'Structure model' struct_conn 7 5 'Structure model' struct_site 8 6 'Structure model' entity 9 6 'Structure model' pdbx_entity_src_syn # 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 4 'Structure model' '_software.name' 2 5 'Structure model' '_database_2.pdbx_DOI' 3 5 'Structure model' '_database_2.pdbx_database_accession' 4 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 5 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_comp_id' 6 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 7 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 8 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_atom_id' 9 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_comp_id' 10 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 11 5 'Structure model' '_pdbx_struct_conn_angle.ptnr1_symmetry' 12 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 13 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 14 5 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 15 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 16 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_comp_id' 17 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 18 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 19 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_atom_id' 20 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_comp_id' 21 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_seq_id' 22 5 'Structure model' '_pdbx_struct_conn_angle.ptnr3_symmetry' 23 5 'Structure model' '_pdbx_struct_conn_angle.value' 24 5 'Structure model' '_struct_conn.pdbx_dist_value' 25 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 26 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 27 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 28 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 29 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 30 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 31 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 32 5 'Structure model' '_struct_conn.ptnr1_symmetry' 33 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 34 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 35 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 36 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 37 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 38 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 39 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 40 5 'Structure model' '_struct_conn.ptnr2_symmetry' 41 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 42 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 43 5 'Structure model' '_struct_site.pdbx_auth_seq_id' 44 6 'Structure model' '_entity.details' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1FD5 _pdbx_database_status.recvd_initial_deposition_date 2000-07-19 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Yang, X.-L.' 1 'Robinson, H.' 2 'Gao, Y.-G.' 3 'Wang, A.H.-J.' 4 # _citation.id primary _citation.title 'Binding of a macrocyclic bisacridine and ametantrone to CGTACG involves similar unusual intercalation platforms.' _citation.journal_abbrev Biochemistry _citation.journal_volume 39 _citation.page_first 10950 _citation.page_last 10957 _citation.year 2000 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10998231 _citation.pdbx_database_id_DOI 10.1021/bi001319z # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Yang, X.L.' 1 ? primary 'Robinson, H.' 2 ? primary 'Gao, Y.G.' 3 ? primary 'Wang, A.H.' 4 ? # 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(*CP*GP*TP*AP*CP*G)-3') ; 1809.217 2 ? ? ? ? 2 non-polymer syn 'COBALT (II) ION' 58.933 2 ? ? ? 'synthetic compound' 3 non-polymer syn MACROCYCLIC-BIS-9-AMINO-ACRIDINE 819.135 1 ? ? ? ? 4 non-polymer syn 'MAGNESIUM ION' 24.305 1 ? ? ? ? 5 water nat water 18.015 74 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type polydeoxyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code '(DC)(DG)(DT)(DA)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGTACG _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'COBALT (II) ION' CO 3 MACROCYCLIC-BIS-9-AMINO-ACRIDINE B9A 4 'MAGNESIUM ION' MG 5 water HOH # 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 DC 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 ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific ? _pdbx_entity_src_syn.organism_common_name ? _pdbx_entity_src_syn.ncbi_taxonomy_id ? _pdbx_entity_src_syn.details 'synthetic DNA moleclue' # 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 B9A non-polymer . MACROCYCLIC-BIS-9-AMINO-ACRIDINE ? 'C46 H58 N8 O2 S2' 819.135 CO non-polymer . 'COBALT (II) ION' ? 'Co 2' 58.933 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 HOH non-polymer . WATER ? 'H2 O' 18.015 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 # 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 C A . n A 1 2 DG 2 2 2 DG G A . n A 1 3 DT 3 3 3 DT T A . n A 1 4 DA 4 4 4 DA A A . n A 1 5 DC 5 5 5 DC C A . n A 1 6 DG 6 6 6 DG G A . n B 1 1 DC 1 7 7 DC C B . n B 1 2 DG 2 8 8 DG G B . n B 1 3 DT 3 9 9 DT T B . n B 1 4 DA 4 10 10 DA A B . n B 1 5 DC 5 11 11 DC C B . n B 1 6 DG 6 12 12 DG G B . 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 C 2 CO 1 21 21 CO CO5 A . D 3 B9A 1 13 13 B9A TMR A . E 2 CO 1 22 22 CO COS B . F 4 MG 1 23 23 MG MG2 B . G 5 HOH 1 103 103 HOH HOH A . G 5 HOH 2 105 105 HOH HOH A . G 5 HOH 3 106 106 HOH HOH A . G 5 HOH 4 108 108 HOH HOH A . G 5 HOH 5 109 109 HOH HOH A . G 5 HOH 6 110 110 HOH HOH A . G 5 HOH 7 118 118 HOH HOH A . G 5 HOH 8 119 119 HOH HOH A . G 5 HOH 9 122 122 HOH HOH A . G 5 HOH 10 124 124 HOH HOH A . G 5 HOH 11 126 126 HOH HOH A . G 5 HOH 12 127 127 HOH HOH A . G 5 HOH 13 128 128 HOH HOH A . G 5 HOH 14 130 130 HOH HOH A . G 5 HOH 15 132 132 HOH HOH A . G 5 HOH 16 134 134 HOH HOH A . G 5 HOH 17 135 135 HOH HOH A . G 5 HOH 18 136 136 HOH HOH A . G 5 HOH 19 138 138 HOH HOH A . G 5 HOH 20 141 141 HOH HOH A . G 5 HOH 21 143 143 HOH HOH A . G 5 HOH 22 144 144 HOH HOH A . G 5 HOH 23 145 145 HOH HOH A . G 5 HOH 24 146 146 HOH HOH A . G 5 HOH 25 152 152 HOH HOH A . G 5 HOH 26 153 153 HOH HOH A . G 5 HOH 27 155 155 HOH HOH A . G 5 HOH 28 157 157 HOH HOH A . G 5 HOH 29 160 160 HOH HOH A . G 5 HOH 30 161 161 HOH HOH A . G 5 HOH 31 162 162 HOH HOH A . G 5 HOH 32 165 165 HOH HOH A . G 5 HOH 33 169 169 HOH HOH A . G 5 HOH 34 174 21 HOH CO5 A . G 5 HOH 35 175 21 HOH CO5 A . G 5 HOH 36 176 21 HOH CO5 A . G 5 HOH 37 177 21 HOH CO5 A . G 5 HOH 38 178 21 HOH CO5 A . H 5 HOH 1 101 101 HOH HOH B . H 5 HOH 2 102 102 HOH HOH B . H 5 HOH 3 104 104 HOH HOH B . H 5 HOH 4 107 107 HOH HOH B . H 5 HOH 5 111 111 HOH HOH B . H 5 HOH 6 112 112 HOH HOH B . H 5 HOH 7 113 113 HOH HOH B . H 5 HOH 8 114 114 HOH HOH B . H 5 HOH 9 115 115 HOH HOH B . H 5 HOH 10 116 116 HOH HOH B . H 5 HOH 11 117 117 HOH HOH B . H 5 HOH 12 120 120 HOH HOH B . H 5 HOH 13 123 123 HOH HOH B . H 5 HOH 14 125 125 HOH HOH B . H 5 HOH 15 129 129 HOH HOH B . H 5 HOH 16 131 131 HOH HOH B . H 5 HOH 17 133 133 HOH HOH B . H 5 HOH 18 137 137 HOH HOH B . H 5 HOH 19 139 139 HOH HOH B . H 5 HOH 20 140 140 HOH HOH B . H 5 HOH 21 142 142 HOH HOH B . H 5 HOH 22 147 147 HOH HOH B . H 5 HOH 23 148 148 HOH HOH B . H 5 HOH 24 149 149 HOH HOH B . H 5 HOH 25 150 150 HOH HOH B . H 5 HOH 26 151 151 HOH HOH B . H 5 HOH 27 154 154 HOH HOH B . H 5 HOH 28 156 156 HOH HOH B . H 5 HOH 29 158 158 HOH HOH B . H 5 HOH 30 163 163 HOH HOH B . H 5 HOH 31 164 164 HOH HOH B . H 5 HOH 32 166 166 HOH HOH B . H 5 HOH 33 170 22 HOH COS B . H 5 HOH 34 171 22 HOH COS B . H 5 HOH 35 172 23 HOH MG2 B . H 5 HOH 36 173 23 HOH MG2 B . # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A DC 1 ? "O5'" ? A DC 1 "O5'" 2 1 Y 1 A DC 1 ? "C5'" ? A DC 1 "C5'" 3 1 Y 1 A DC 1 ? "C4'" ? A DC 1 "C4'" 4 1 Y 1 A DC 1 ? "O4'" ? A DC 1 "O4'" 5 1 Y 1 A DC 1 ? "C3'" ? A DC 1 "C3'" 6 1 Y 1 A DC 1 ? "C2'" ? A DC 1 "C2'" 7 1 Y 1 A DC 1 ? "C1'" ? A DC 1 "C1'" 8 1 Y 1 A DC 1 ? N1 ? A DC 1 N1 9 1 Y 1 A DC 1 ? C2 ? A DC 1 C2 10 1 Y 1 A DC 1 ? O2 ? A DC 1 O2 11 1 Y 1 A DC 1 ? N3 ? A DC 1 N3 12 1 Y 1 A DC 1 ? C4 ? A DC 1 C4 13 1 Y 1 A DC 1 ? N4 ? A DC 1 N4 14 1 Y 1 A DC 1 ? C5 ? A DC 1 C5 15 1 Y 1 A DC 1 ? C6 ? A DC 1 C6 16 1 N 1 A B9A 13 ? C16 ? D B9A 1 C16 17 1 N 1 A B9A 13 ? C17 ? D B9A 1 C17 18 1 N 1 A B9A 13 ? N18 ? D B9A 1 N18 19 1 N 1 A B9A 13 ? C19 ? D B9A 1 C19 20 1 N 1 A B9A 13 ? C20 ? D B9A 1 C20 21 1 N 1 A B9A 13 ? C21 ? D B9A 1 C21 22 1 N 1 A B9A 13 ? C22 ? D B9A 1 C22 23 1 N 1 A B9A 13 ? N23 ? D B9A 1 N23 24 1 N 1 A B9A 13 ? C24 ? D B9A 1 C24 25 1 N 1 A B9A 13 ? C25 ? D B9A 1 C25 26 1 N 1 A B9A 13 ? C26 ? D B9A 1 C26 27 1 N 1 A B9A 13 ? C28 ? D B9A 1 C28 28 1 N 1 A B9A 13 ? S29 ? D B9A 1 S29 29 1 N 1 A B9A 13 ? C30 ? D B9A 1 C30 30 1 N 1 A B9A 13 ? C31 ? D B9A 1 C31 31 1 N 1 A B9A 13 ? N32 ? D B9A 1 N32 32 1 N 1 A B9A 13 ? C33 ? D B9A 1 C33 33 1 N 1 A B9A 13 ? O34 ? D B9A 1 O34 34 1 N 1 A B9A 13 ? C35 ? D B9A 1 C35 35 1 N 1 A B9A 13 ? C36 ? D B9A 1 C36 36 1 N 1 A B9A 13 ? C37 ? D B9A 1 C37 37 1 N 1 A B9A 13 ? O38 ? D B9A 1 O38 38 1 N 1 A B9A 13 ? N39 ? D B9A 1 N39 39 1 N 1 A B9A 13 ? C40 ? D B9A 1 C40 40 1 N 1 A B9A 13 ? C41 ? D B9A 1 C41 41 1 N 1 A B9A 13 ? S42 ? D B9A 1 S42 42 1 N 1 A B9A 13 ? C43 ? D B9A 1 C43 43 1 N 1 A B9A 13 ? C1B ? D B9A 1 C1B 44 1 N 1 A B9A 13 ? C2B ? D B9A 1 C2B 45 1 N 1 A B9A 13 ? C3B ? D B9A 1 C3B 46 1 N 1 A B9A 13 ? C4B ? D B9A 1 C4B 47 1 N 1 A B9A 13 ? C5B ? D B9A 1 C5B 48 1 N 1 A B9A 13 ? C6B ? D B9A 1 C6B 49 1 N 1 A B9A 13 ? C7B ? D B9A 1 C7B 50 1 N 1 A B9A 13 ? C8B ? D B9A 1 C8B 51 1 N 1 A B9A 13 ? C9B ? D B9A 1 C9B 52 1 N 1 A B9A 13 ? NAB ? D B9A 1 NAB 53 1 N 1 A B9A 13 ? CBB ? D B9A 1 CBB 54 1 N 1 A B9A 13 ? CCB ? D B9A 1 CCB 55 1 N 1 A B9A 13 ? CDB ? D B9A 1 CDB 56 1 N 1 A B9A 13 ? CEB ? D B9A 1 CEB 57 1 N 1 A B9A 13 ? N9B ? D B9A 1 N9B # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELXL-97 refinement . ? 1 CNS refinement . ? 2 d*TREK 'data reduction' . ? 3 HKL-2000 'data scaling' . ? 4 CNS phasing . ? 5 # _cell.entry_id 1FD5 _cell.length_a 29.584 _cell.length_b 54.038 _cell.length_c 40.215 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1FD5 _symmetry.space_group_name_H-M 'C 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 # _exptl.entry_id 1FD5 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 2 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 42.17 _exptl_crystal.density_Matthews 2.13 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 6.0 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details ;MPD, sodium cacodylate buffer, magnesium chloride, cobalt chloride, spermine, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 110 ? 1 2 110 ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD CUSTOM-MADE 1999-08-28 ? 2 CCD CUSTOM-MADE 2000-02-05 ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.7251 1.0 2 0.9199 1.0 3 0.9200 1.0 4 0.8856 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'APS BEAMLINE 19-ID' ? APS 19-ID '0.7251, 0.9199, 0.9200,0.8856' 2 SYNCHROTRON 'APS BEAMLINE 19-ID' ? APS 19-ID ? # _reflns.entry_id 1FD5 _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 100 _reflns.d_resolution_high 1.1 _reflns.number_obs 196823 _reflns.number_all 196823 _reflns.percent_possible_obs 99.9 _reflns.pdbx_Rmerge_I_obs 0.0570000 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 40.5 _reflns.B_iso_Wilson_estimate 23.0 _reflns.pdbx_redundancy 9.4 _reflns.R_free_details ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.10 _reflns_shell.d_res_low 1.14 _reflns_shell.percent_possible_obs ? _reflns_shell.percent_possible_all 100 _reflns_shell.Rmerge_I_obs 0.5970000 _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_Rsym_value ? _reflns_shell.pdbx_redundancy 7.2 _reflns_shell.number_unique_all 1293 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1FD5 _refine.ls_number_reflns_obs 10911 _refine.ls_number_reflns_all 12702 _refine.pdbx_ls_sigma_I 2 _refine.pdbx_ls_sigma_F 4 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 10 _refine.ls_d_res_high 1.1 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1680000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1630000 _refine.ls_R_factor_R_free 0.2030000 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 544 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'G.PARKINSON, J.VOJTECHOVSKY, L.CLOWNEY, A.T.BRUNGER, H.M.BERMAN' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details random _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 225 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 318 _refine_hist.d_res_high 1.1 _refine_hist.d_res_low 10 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.014 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 2.0 ? ? ? 'X-RAY DIFFRACTION' ? # _database_PDB_matrix.entry_id 1FD5 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _struct.entry_id 1FD5 _struct.title ;BINDING OF A MACROCYCLIC BISACRIDINE AND AMETANTRONE TO CGTACG INVOLVES SIMILAR UNUSUAL INTERCALATION PLATFORMS (BISACRIDINE COMPLEX) ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1FD5 _struct_keywords.pdbx_keywords DNA _struct_keywords.text ;High resolution crystal structure, intercalation platform, MAD, anticancer drug, drug-DNA complex, metal ions, tertiary base pairs, 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 ? C N N 2 ? D N N 3 ? E N N 2 ? F N N 4 ? G N N 5 ? H N N 5 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1FD5 _struct_ref.pdbx_db_accession 1FD5 _struct_ref.pdbx_db_isoform ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_align_begin ? # 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 1FD5 A 1 ? 6 ? 1FD5 1 ? 6 ? 1 6 2 1 1FD5 B 1 ? 6 ? 1FD5 7 ? 12 ? 7 12 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_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,C,D,E,F,G,H # _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 x,y,z _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 metalc1 metalc ? ? A DG 2 N7 ? ? ? 1_555 C CO . CO ? ? A DG 2 A CO 21 1_555 ? ? ? ? ? ? ? 2.124 ? ? metalc2 metalc ? ? C CO . CO ? ? ? 1_555 G HOH . O ? ? A CO 21 A HOH 174 1_555 ? ? ? ? ? ? ? 1.997 ? ? metalc3 metalc ? ? C CO . CO ? ? ? 1_555 G HOH . O ? ? A CO 21 A HOH 175 1_555 ? ? ? ? ? ? ? 2.034 ? ? metalc4 metalc ? ? C CO . CO ? ? ? 1_555 G HOH . O ? ? A CO 21 A HOH 176 1_555 ? ? ? ? ? ? ? 1.995 ? ? metalc5 metalc ? ? C CO . CO ? ? ? 1_555 G HOH . O ? ? A CO 21 A HOH 177 1_555 ? ? ? ? ? ? ? 2.024 ? ? metalc6 metalc ? ? C CO . CO ? ? ? 1_555 G HOH . O ? ? A CO 21 A HOH 178 1_555 ? ? ? ? ? ? ? 2.005 ? ? metalc7 metalc ? ? B DG 2 OP2 ? ? ? 1_555 F MG . MG ? ? B DG 8 B MG 23 1_555 ? ? ? ? ? ? ? 2.096 ? ? metalc8 metalc ? ? B DG 2 OP2 ? ? ? 4_556 F MG . MG ? ? B DG 8 B MG 23 1_555 ? ? ? ? ? ? ? 2.096 ? ? metalc9 metalc ? ? B DG 6 N7 ? ? ? 1_555 E CO . CO ? ? B DG 12 B CO 22 1_555 ? ? ? ? ? ? ? 2.173 ? ? metalc10 metalc ? ? B DG 6 N7 ? ? ? 3_755 E CO . CO ? ? B DG 12 B CO 22 1_555 ? ? ? ? ? ? ? 2.173 ? ? metalc11 metalc ? ? E CO . CO ? ? ? 1_555 H HOH . O ? ? B CO 22 B HOH 170 1_555 ? ? ? ? ? ? ? 2.089 ? ? metalc12 metalc ? ? E CO . CO ? ? ? 1_555 H HOH . O ? ? B CO 22 B HOH 170 3_755 ? ? ? ? ? ? ? 2.089 ? ? metalc13 metalc ? ? E CO . CO ? ? ? 1_555 H HOH . O ? ? B CO 22 B HOH 171 1_555 ? ? ? ? ? ? ? 2.022 ? ? metalc14 metalc ? ? E CO . CO ? ? ? 1_555 H HOH . O ? ? B CO 22 B HOH 171 3_755 ? ? ? ? ? ? ? 2.022 ? ? metalc15 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 172 1_555 ? ? ? ? ? ? ? 2.041 ? ? metalc16 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 172 4_556 ? ? ? ? ? ? ? 2.041 ? ? metalc17 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 172 3_656 ? ? ? ? ? ? ? 1.865 ? ? metalc18 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 172 2_655 ? ? ? ? ? ? ? 1.865 ? ? metalc19 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 173 1_555 ? ? ? ? ? ? ? 2.049 ? ? metalc20 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 173 4_556 ? ? ? ? ? ? ? 2.050 ? ? hydrog1 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 5 N3 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 5 O2 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 5 N4 ? ? A DG 2 B DC 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DT 3 N3 ? ? ? 1_555 B DA 4 N1 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DT 3 O4 ? ? ? 1_555 B DA 4 N6 ? ? A DT 3 B DA 10 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DA 4 N1 ? ? ? 1_555 B DT 3 N3 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DA 4 N6 ? ? ? 1_555 B DT 3 O4 ? ? A DA 4 B DT 9 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 5 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 5 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DC 5 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 5 B DG 8 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference 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 N7 ? A DG 2 ? A DG 2 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 174 ? 1_555 95.6 ? 2 N7 ? A DG 2 ? A DG 2 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 175 ? 1_555 89.9 ? 3 O ? G HOH . ? A HOH 174 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 175 ? 1_555 89.6 ? 4 N7 ? A DG 2 ? A DG 2 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 176 ? 1_555 94.1 ? 5 O ? G HOH . ? A HOH 174 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 176 ? 1_555 89.0 ? 6 O ? G HOH . ? A HOH 175 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 176 ? 1_555 175.8 ? 7 N7 ? A DG 2 ? A DG 2 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 177 ? 1_555 86.0 ? 8 O ? G HOH . ? A HOH 174 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 177 ? 1_555 178.1 ? 9 O ? G HOH . ? A HOH 175 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 177 ? 1_555 89.5 ? 10 O ? G HOH . ? A HOH 176 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 177 ? 1_555 91.8 ? 11 N7 ? A DG 2 ? A DG 2 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 178 ? 1_555 175.4 ? 12 O ? G HOH . ? A HOH 174 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 178 ? 1_555 88.7 ? 13 O ? G HOH . ? A HOH 175 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 178 ? 1_555 88.7 ? 14 O ? G HOH . ? A HOH 176 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 178 ? 1_555 87.3 ? 15 O ? G HOH . ? A HOH 177 ? 1_555 CO ? C CO . ? A CO 21 ? 1_555 O ? G HOH . ? A HOH 178 ? 1_555 89.6 ? 16 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 OP2 ? B DG 2 ? B DG 8 ? 4_556 97.3 ? 17 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 1_555 88.1 ? 18 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 1_555 173.6 ? 19 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 4_556 173.5 ? 20 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 4_556 88.1 ? 21 O ? H HOH . ? B HOH 172 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 4_556 86.8 ? 22 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 3_656 89.7 ? 23 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 3_656 151.2 ? 24 O ? H HOH . ? B HOH 172 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 3_656 31.6 ? 25 O ? H HOH . ? B HOH 172 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 3_656 83.9 ? 26 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 2_655 151.3 ? 27 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 2_655 89.7 ? 28 O ? H HOH . ? B HOH 172 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 2_655 83.9 ? 29 O ? H HOH . ? B HOH 172 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 2_655 31.6 ? 30 O ? H HOH . ? B HOH 172 ? 3_656 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 172 ? 2_655 97.5 ? 31 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 98.2 ? 32 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 81.2 ? 33 O ? H HOH . ? B HOH 172 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 94.5 ? 34 O ? H HOH . ? B HOH 172 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 86.1 ? 35 O ? H HOH . ? B HOH 172 ? 3_656 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 125.5 ? 36 O ? H HOH . ? B HOH 172 ? 2_655 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 1_555 55.2 ? 37 OP2 ? B DG 2 ? B DG 8 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 81.2 ? 38 OP2 ? B DG 2 ? B DG 8 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 98.2 ? 39 O ? H HOH . ? B HOH 172 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 86.1 ? 40 O ? H HOH . ? B HOH 172 ? 4_556 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 94.5 ? 41 O ? H HOH . ? B HOH 172 ? 3_656 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 55.2 ? 42 O ? H HOH . ? B HOH 172 ? 2_655 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 125.5 ? 43 O ? H HOH . ? B HOH 173 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 173 ? 4_556 179.1 ? 44 N7 ? B DG 6 ? B DG 12 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 N7 ? B DG 6 ? B DG 12 ? 3_755 178.7 ? 45 N7 ? B DG 6 ? B DG 12 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 170 ? 1_555 86.7 ? 46 N7 ? B DG 6 ? B DG 12 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 170 ? 1_555 92.3 ? 47 N7 ? B DG 6 ? B DG 12 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 170 ? 3_755 92.3 ? 48 N7 ? B DG 6 ? B DG 12 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 170 ? 3_755 86.7 ? 49 O ? H HOH . ? B HOH 170 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 170 ? 3_755 85.4 ? 50 N7 ? B DG 6 ? B DG 12 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 1_555 91.7 ? 51 N7 ? B DG 6 ? B DG 12 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 1_555 89.1 ? 52 O ? H HOH . ? B HOH 170 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 1_555 88.4 ? 53 O ? H HOH . ? B HOH 170 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 1_555 172.3 ? 54 N7 ? B DG 6 ? B DG 12 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 3_755 89.1 ? 55 N7 ? B DG 6 ? B DG 12 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 3_755 91.7 ? 56 O ? H HOH . ? B HOH 170 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 3_755 172.3 ? 57 O ? H HOH . ? B HOH 170 ? 3_755 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 3_755 88.4 ? 58 O ? H HOH . ? B HOH 171 ? 1_555 CO ? E CO . ? B CO 22 ? 1_555 O ? H HOH . ? B HOH 171 ? 3_755 98.2 ? # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software B CO 22 ? 6 'BINDING SITE FOR RESIDUE CO B 22' AC2 Software B MG 23 ? 8 'BINDING SITE FOR RESIDUE MG B 23' AC3 Software A CO 21 ? 6 'BINDING SITE FOR RESIDUE CO A 21' AC4 Software A B9A 13 ? 4 'BINDING SITE FOR RESIDUE B9A A 13' 1 ? ? ? ? ? ? ? # loop_ _struct_site_gen.id _struct_site_gen.site_id _struct_site_gen.pdbx_num_res _struct_site_gen.label_comp_id _struct_site_gen.label_asym_id _struct_site_gen.label_seq_id _struct_site_gen.pdbx_auth_ins_code _struct_site_gen.auth_comp_id _struct_site_gen.auth_asym_id _struct_site_gen.auth_seq_id _struct_site_gen.label_atom_id _struct_site_gen.label_alt_id _struct_site_gen.symmetry _struct_site_gen.details 1 AC1 6 DG B 6 ? DG B 12 . ? 3_755 ? 2 AC1 6 DG B 6 ? DG B 12 . ? 1_555 ? 3 AC1 6 HOH H . ? HOH B 170 . ? 3_755 ? 4 AC1 6 HOH H . ? HOH B 170 . ? 1_555 ? 5 AC1 6 HOH H . ? HOH B 171 . ? 3_755 ? 6 AC1 6 HOH H . ? HOH B 171 . ? 1_555 ? 7 AC2 8 DG B 2 ? DG B 8 . ? 4_556 ? 8 AC2 8 DG B 2 ? DG B 8 . ? 1_555 ? 9 AC2 8 HOH H . ? HOH B 172 . ? 1_555 ? 10 AC2 8 HOH H . ? HOH B 172 . ? 3_656 ? 11 AC2 8 HOH H . ? HOH B 172 . ? 2_655 ? 12 AC2 8 HOH H . ? HOH B 172 . ? 4_556 ? 13 AC2 8 HOH H . ? HOH B 173 . ? 4_556 ? 14 AC2 8 HOH H . ? HOH B 173 . ? 1_555 ? 15 AC3 6 DG A 2 ? DG A 2 . ? 1_555 ? 16 AC3 6 HOH G . ? HOH A 174 . ? 1_555 ? 17 AC3 6 HOH G . ? HOH A 175 . ? 1_555 ? 18 AC3 6 HOH G . ? HOH A 176 . ? 1_555 ? 19 AC3 6 HOH G . ? HOH A 177 . ? 1_555 ? 20 AC3 6 HOH G . ? HOH A 178 . ? 1_555 ? 21 AC4 4 DC A 5 ? DC A 5 . ? 1_555 ? 22 AC4 4 DG A 6 ? DG A 6 . ? 1_555 ? 23 AC4 4 DC B 1 ? DC B 7 . ? 3_656 ? 24 AC4 4 DG B 2 ? DG B 8 . ? 1_555 ? # 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 N1 A DA 4 ? ? C2 A DA 4 ? ? N3 A DA 4 ? ? 124.35 129.30 -4.95 0.50 N 2 1 C2 A DA 4 ? ? N3 A DA 4 ? ? C4 A DA 4 ? ? 114.22 110.60 3.62 0.50 N 3 1 "O5'" A DG 6 ? ? "C5'" A DG 6 ? ? "C4'" A DG 6 ? ? 104.03 109.40 -5.37 0.80 N 4 1 N3 A DG 6 ? ? C2 A DG 6 ? ? N2 A DG 6 ? ? 115.70 119.90 -4.20 0.70 N 5 1 "O4'" B DC 7 ? ? "C1'" B DC 7 ? ? N1 B DC 7 ? ? 102.55 108.00 -5.45 0.70 N 6 1 C5 B DA 10 ? ? N7 B DA 10 ? ? C8 B DA 10 ? ? 106.99 103.90 3.09 0.50 N 7 1 N7 B DA 10 ? ? C8 B DA 10 ? ? N9 B DA 10 ? ? 110.38 113.80 -3.42 0.50 N 8 1 "O4'" B DG 12 ? ? "C1'" B DG 12 ? ? N9 B DG 12 ? ? 110.54 108.30 2.24 0.30 N 9 1 N1 B DG 12 ? ? C6 B DG 12 ? ? O6 B DG 12 ? ? 115.95 119.90 -3.95 0.60 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 B 8 ? ? 0.067 'SIDE CHAIN' 2 1 DG B 12 ? ? 0.064 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text INTERCALATION # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 B CO 22 ? E CO . 2 1 B MG 23 ? F MG . 3 1 A HOH 134 ? G HOH . 4 1 B HOH 102 ? H HOH . 5 1 B HOH 149 ? H HOH . 6 1 B HOH 158 ? H HOH . # 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 B9A C1A C Y N 1 B9A C2A C Y N 2 B9A C3A C Y N 3 B9A C4A C Y N 4 B9A C5A C Y N 5 B9A C6A C Y N 6 B9A C7A C Y N 7 B9A C8A C Y N 8 B9A C9A C Y N 9 B9A N9A N N N 10 B9A NAA N Y N 11 B9A CBA C Y N 12 B9A CCA C Y N 13 B9A CDA C Y N 14 B9A CEA C Y N 15 B9A C15 C N N 16 B9A C16 C N N 17 B9A C17 C N N 18 B9A N18 N N N 19 B9A C19 C N N 20 B9A C20 C N N 21 B9A C21 C N N 22 B9A C22 C N N 23 B9A N23 N N N 24 B9A C24 C N N 25 B9A C25 C N N 26 B9A C26 C N N 27 B9A C28 C N N 28 B9A S29 S N N 29 B9A C30 C N N 30 B9A C31 C N N 31 B9A N32 N N N 32 B9A C33 C N N 33 B9A O34 O N N 34 B9A C35 C N N 35 B9A C36 C N N 36 B9A C37 C N N 37 B9A O38 O N N 38 B9A N39 N N N 39 B9A C40 C N N 40 B9A C41 C N N 41 B9A S42 S N N 42 B9A C43 C N N 43 B9A C1B C Y N 44 B9A C2B C Y N 45 B9A C3B C Y N 46 B9A C4B C Y N 47 B9A C5B C Y N 48 B9A C6B C Y N 49 B9A C7B C Y N 50 B9A C8B C Y N 51 B9A C9B C Y N 52 B9A NAB N Y N 53 B9A CBB C Y N 54 B9A CCB C Y N 55 B9A CDB C Y N 56 B9A CEB C Y N 57 B9A N9B N N N 58 B9A H1A H N N 59 B9A H2A H N N 60 B9A H3A H N N 61 B9A H5A H N N 62 B9A H6A H N N 63 B9A H7A H N N 64 B9A H8A H N N 65 B9A H9A H N N 66 B9A H151 H N N 67 B9A H152 H N N 68 B9A H161 H N N 69 B9A H162 H N N 70 B9A H171 H N N 71 B9A H172 H N N 72 B9A H18 H N N 73 B9A H191 H N N 74 B9A H192 H N N 75 B9A H201 H N N 76 B9A H202 H N N 77 B9A H211 H N N 78 B9A H212 H N N 79 B9A H221 H N N 80 B9A H222 H N N 81 B9A H23 H N N 82 B9A H241 H N N 83 B9A H242 H N N 84 B9A H251 H N N 85 B9A H252 H N N 86 B9A H261 H N N 87 B9A H262 H N N 88 B9A H281 H N N 89 B9A H282 H N N 90 B9A H301 H N N 91 B9A H302 H N N 92 B9A H311 H N N 93 B9A H312 H N N 94 B9A H32 H N N 95 B9A H351 H N N 96 B9A H352 H N N 97 B9A H361 H N N 98 B9A H362 H N N 99 B9A HC37 H N N 100 B9A HO38 H N N 101 B9A H39 H N N 102 B9A H401 H N N 103 B9A H402 H N N 104 B9A H411 H N N 105 B9A H412 H N N 106 B9A H431 H N N 107 B9A H432 H N N 108 B9A H1B H N N 109 B9A H2B H N N 110 B9A H3B H N N 111 B9A H4B H N N 112 B9A H6B H N N 113 B9A H7B H N N 114 B9A H8B H N N 115 B9A H9B H N N 116 CO CO CO N N 117 DA OP3 O N N 118 DA P P N N 119 DA OP1 O N N 120 DA OP2 O N N 121 DA "O5'" O N N 122 DA "C5'" C N N 123 DA "C4'" C N R 124 DA "O4'" O N N 125 DA "C3'" C N S 126 DA "O3'" O N N 127 DA "C2'" C N N 128 DA "C1'" C N R 129 DA N9 N Y N 130 DA C8 C Y N 131 DA N7 N Y N 132 DA C5 C Y N 133 DA C6 C Y N 134 DA N6 N N N 135 DA N1 N Y N 136 DA C2 C Y N 137 DA N3 N Y N 138 DA C4 C Y N 139 DA HOP3 H N N 140 DA HOP2 H N N 141 DA "H5'" H N N 142 DA "H5''" H N N 143 DA "H4'" H N N 144 DA "H3'" H N N 145 DA "HO3'" H N N 146 DA "H2'" H N N 147 DA "H2''" H N N 148 DA "H1'" H N N 149 DA H8 H N N 150 DA H61 H N N 151 DA H62 H N N 152 DA H2 H N N 153 DC OP3 O N N 154 DC P P N N 155 DC OP1 O N N 156 DC OP2 O N N 157 DC "O5'" O N N 158 DC "C5'" C N N 159 DC "C4'" C N R 160 DC "O4'" O N N 161 DC "C3'" C N S 162 DC "O3'" O N N 163 DC "C2'" C N N 164 DC "C1'" C N R 165 DC N1 N N N 166 DC C2 C N N 167 DC O2 O N N 168 DC N3 N N N 169 DC C4 C N N 170 DC N4 N N N 171 DC C5 C N N 172 DC C6 C N N 173 DC HOP3 H N N 174 DC HOP2 H N N 175 DC "H5'" H N N 176 DC "H5''" H N N 177 DC "H4'" H N N 178 DC "H3'" H N N 179 DC "HO3'" H N N 180 DC "H2'" H N N 181 DC "H2''" H N N 182 DC "H1'" H N N 183 DC H41 H N N 184 DC H42 H N N 185 DC H5 H N N 186 DC H6 H N N 187 DG OP3 O N N 188 DG P P N N 189 DG OP1 O N N 190 DG OP2 O N N 191 DG "O5'" O N N 192 DG "C5'" C N N 193 DG "C4'" C N R 194 DG "O4'" O N N 195 DG "C3'" C N S 196 DG "O3'" O N N 197 DG "C2'" C N N 198 DG "C1'" C N R 199 DG N9 N Y N 200 DG C8 C Y N 201 DG N7 N Y N 202 DG C5 C Y N 203 DG C6 C N N 204 DG O6 O N N 205 DG N1 N N N 206 DG C2 C N N 207 DG N2 N N N 208 DG N3 N N N 209 DG C4 C Y N 210 DG HOP3 H N N 211 DG HOP2 H N N 212 DG "H5'" H N N 213 DG "H5''" H N N 214 DG "H4'" H N N 215 DG "H3'" H N N 216 DG "HO3'" H N N 217 DG "H2'" H N N 218 DG "H2''" H N N 219 DG "H1'" H N N 220 DG H8 H N N 221 DG H1 H N N 222 DG H21 H N N 223 DG H22 H N N 224 DT OP3 O N N 225 DT P P N N 226 DT OP1 O N N 227 DT OP2 O N N 228 DT "O5'" O N N 229 DT "C5'" C N N 230 DT "C4'" C N R 231 DT "O4'" O N N 232 DT "C3'" C N S 233 DT "O3'" O N N 234 DT "C2'" C N N 235 DT "C1'" C N R 236 DT N1 N N N 237 DT C2 C N N 238 DT O2 O N N 239 DT N3 N N N 240 DT C4 C N N 241 DT O4 O N N 242 DT C5 C N N 243 DT C7 C N N 244 DT C6 C N N 245 DT HOP3 H N N 246 DT HOP2 H N N 247 DT "H5'" H N N 248 DT "H5''" H N N 249 DT "H4'" H N N 250 DT "H3'" H N N 251 DT "HO3'" H N N 252 DT "H2'" H N N 253 DT "H2''" H N N 254 DT "H1'" H N N 255 DT H3 H N N 256 DT H71 H N N 257 DT H72 H N N 258 DT H73 H N N 259 DT H6 H N N 260 HOH O O N N 261 HOH H1 H N N 262 HOH H2 H N N 263 MG MG MG N N 264 # 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 B9A C1A C2A doub Y N 1 B9A C1A CDA sing Y N 2 B9A C1A H1A sing N N 3 B9A C2A C3A sing Y N 4 B9A C2A H2A sing N N 5 B9A C3A C4A doub Y N 6 B9A C3A H3A sing N N 7 B9A C4A CEA sing Y N 8 B9A C4A C28 sing N N 9 B9A C5A C6A doub Y N 10 B9A C5A CBA sing Y N 11 B9A C5A H5A sing N N 12 B9A C6A C7A sing Y N 13 B9A C6A H6A sing N N 14 B9A C7A C8A doub Y N 15 B9A C7A H7A sing N N 16 B9A C8A CCA sing Y N 17 B9A C8A H8A sing N N 18 B9A C9A N9A sing N N 19 B9A C9A CCA doub Y N 20 B9A C9A CDA sing Y N 21 B9A N9A C15 sing N N 22 B9A N9A H9A sing N N 23 B9A NAA CBA doub Y N 24 B9A NAA CEA sing Y N 25 B9A CBA CCA sing Y N 26 B9A CDA CEA doub Y N 27 B9A C15 C16 sing N N 28 B9A C15 H151 sing N N 29 B9A C15 H152 sing N N 30 B9A C16 C17 sing N N 31 B9A C16 H161 sing N N 32 B9A C16 H162 sing N N 33 B9A C17 N18 sing N N 34 B9A C17 H171 sing N N 35 B9A C17 H172 sing N N 36 B9A N18 C19 sing N N 37 B9A N18 H18 sing N N 38 B9A C19 C20 sing N N 39 B9A C19 H191 sing N N 40 B9A C19 H192 sing N N 41 B9A C20 C21 sing N N 42 B9A C20 H201 sing N N 43 B9A C20 H202 sing N N 44 B9A C21 C22 sing N N 45 B9A C21 H211 sing N N 46 B9A C21 H212 sing N N 47 B9A C22 N23 sing N N 48 B9A C22 H221 sing N N 49 B9A C22 H222 sing N N 50 B9A N23 C24 sing N N 51 B9A N23 H23 sing N N 52 B9A C24 C25 sing N N 53 B9A C24 H241 sing N N 54 B9A C24 H242 sing N N 55 B9A C25 C26 sing N N 56 B9A C25 H251 sing N N 57 B9A C25 H252 sing N N 58 B9A C26 N9B sing N N 59 B9A C26 H261 sing N N 60 B9A C26 H262 sing N N 61 B9A C28 S29 sing N N 62 B9A C28 H281 sing N N 63 B9A C28 H282 sing N N 64 B9A S29 C30 sing N N 65 B9A C30 C31 sing N N 66 B9A C30 H301 sing N N 67 B9A C30 H302 sing N N 68 B9A C31 N32 sing N N 69 B9A C31 H311 sing N N 70 B9A C31 H312 sing N N 71 B9A N32 C33 sing N N 72 B9A N32 H32 sing N N 73 B9A C33 O34 doub N N 74 B9A C33 C35 sing N N 75 B9A C35 C36 sing N N 76 B9A C35 H351 sing N N 77 B9A C35 H352 sing N N 78 B9A C36 C37 sing N N 79 B9A C36 H361 sing N N 80 B9A C36 H362 sing N N 81 B9A C37 O38 sing N N 82 B9A C37 N39 sing N N 83 B9A C37 HC37 sing N N 84 B9A O38 HO38 sing N N 85 B9A N39 C40 sing N N 86 B9A N39 H39 sing N N 87 B9A C40 C41 sing N N 88 B9A C40 H401 sing N N 89 B9A C40 H402 sing N N 90 B9A C41 S42 sing N N 91 B9A C41 H411 sing N N 92 B9A C41 H412 sing N N 93 B9A S42 C43 sing N N 94 B9A C43 C5B sing N N 95 B9A C43 H431 sing N N 96 B9A C43 H432 sing N N 97 B9A C1B C2B doub Y N 98 B9A C1B CDB sing Y N 99 B9A C1B H1B sing N N 100 B9A C2B C3B sing Y N 101 B9A C2B H2B sing N N 102 B9A C3B C4B doub Y N 103 B9A C3B H3B sing N N 104 B9A C4B CEB sing Y N 105 B9A C4B H4B sing N N 106 B9A C5B C6B doub Y N 107 B9A C5B CBB sing Y N 108 B9A C6B C7B sing Y N 109 B9A C6B H6B sing N N 110 B9A C7B C8B doub Y N 111 B9A C7B H7B sing N N 112 B9A C8B CCB sing Y N 113 B9A C8B H8B sing N N 114 B9A C9B CCB doub Y N 115 B9A C9B CDB sing Y N 116 B9A C9B N9B sing N N 117 B9A NAB CBB doub Y N 118 B9A NAB CEB sing Y N 119 B9A CBB CCB sing Y N 120 B9A CDB CEB doub Y N 121 B9A N9B H9B sing N N 122 DA OP3 P sing N N 123 DA OP3 HOP3 sing N N 124 DA P OP1 doub N N 125 DA P OP2 sing N N 126 DA P "O5'" sing N N 127 DA OP2 HOP2 sing N N 128 DA "O5'" "C5'" sing N N 129 DA "C5'" "C4'" sing N N 130 DA "C5'" "H5'" sing N N 131 DA "C5'" "H5''" sing N N 132 DA "C4'" "O4'" sing N N 133 DA "C4'" "C3'" sing N N 134 DA "C4'" "H4'" sing N N 135 DA "O4'" "C1'" sing N N 136 DA "C3'" "O3'" sing N N 137 DA "C3'" "C2'" sing N N 138 DA "C3'" "H3'" sing N N 139 DA "O3'" "HO3'" sing N N 140 DA "C2'" "C1'" sing N N 141 DA "C2'" "H2'" sing N N 142 DA "C2'" "H2''" sing N N 143 DA "C1'" N9 sing N N 144 DA "C1'" "H1'" sing N N 145 DA N9 C8 sing Y N 146 DA N9 C4 sing Y N 147 DA C8 N7 doub Y N 148 DA C8 H8 sing N N 149 DA N7 C5 sing Y N 150 DA C5 C6 sing Y N 151 DA C5 C4 doub Y N 152 DA C6 N6 sing N N 153 DA C6 N1 doub Y N 154 DA N6 H61 sing N N 155 DA N6 H62 sing N N 156 DA N1 C2 sing Y N 157 DA C2 N3 doub Y N 158 DA C2 H2 sing N N 159 DA N3 C4 sing Y N 160 DC OP3 P sing N N 161 DC OP3 HOP3 sing N N 162 DC P OP1 doub N N 163 DC P OP2 sing N N 164 DC P "O5'" sing N N 165 DC OP2 HOP2 sing N N 166 DC "O5'" "C5'" sing N N 167 DC "C5'" "C4'" sing N N 168 DC "C5'" "H5'" sing N N 169 DC "C5'" "H5''" sing N N 170 DC "C4'" "O4'" sing N N 171 DC "C4'" "C3'" sing N N 172 DC "C4'" "H4'" sing N N 173 DC "O4'" "C1'" sing N N 174 DC "C3'" "O3'" sing N N 175 DC "C3'" "C2'" sing N N 176 DC "C3'" "H3'" sing N N 177 DC "O3'" "HO3'" sing N N 178 DC "C2'" "C1'" sing N N 179 DC "C2'" "H2'" sing N N 180 DC "C2'" "H2''" sing N N 181 DC "C1'" N1 sing N N 182 DC "C1'" "H1'" sing N N 183 DC N1 C2 sing N N 184 DC N1 C6 sing N N 185 DC C2 O2 doub N N 186 DC C2 N3 sing N N 187 DC N3 C4 doub N N 188 DC C4 N4 sing N N 189 DC C4 C5 sing N N 190 DC N4 H41 sing N N 191 DC N4 H42 sing N N 192 DC C5 C6 doub N N 193 DC C5 H5 sing N N 194 DC C6 H6 sing N N 195 DG OP3 P sing N N 196 DG OP3 HOP3 sing N N 197 DG P OP1 doub N N 198 DG P OP2 sing N N 199 DG P "O5'" sing N N 200 DG OP2 HOP2 sing N N 201 DG "O5'" "C5'" sing N N 202 DG "C5'" "C4'" sing N N 203 DG "C5'" "H5'" sing N N 204 DG "C5'" "H5''" sing N N 205 DG "C4'" "O4'" sing N N 206 DG "C4'" "C3'" sing N N 207 DG "C4'" "H4'" sing N N 208 DG "O4'" "C1'" sing N N 209 DG "C3'" "O3'" sing N N 210 DG "C3'" "C2'" sing N N 211 DG "C3'" "H3'" sing N N 212 DG "O3'" "HO3'" sing N N 213 DG "C2'" "C1'" sing N N 214 DG "C2'" "H2'" sing N N 215 DG "C2'" "H2''" sing N N 216 DG "C1'" N9 sing N N 217 DG "C1'" "H1'" sing N N 218 DG N9 C8 sing Y N 219 DG N9 C4 sing Y N 220 DG C8 N7 doub Y N 221 DG C8 H8 sing N N 222 DG N7 C5 sing Y N 223 DG C5 C6 sing N N 224 DG C5 C4 doub Y N 225 DG C6 O6 doub N N 226 DG C6 N1 sing N N 227 DG N1 C2 sing N N 228 DG N1 H1 sing N N 229 DG C2 N2 sing N N 230 DG C2 N3 doub N N 231 DG N2 H21 sing N N 232 DG N2 H22 sing N N 233 DG N3 C4 sing N N 234 DT OP3 P sing N N 235 DT OP3 HOP3 sing N N 236 DT P OP1 doub N N 237 DT P OP2 sing N N 238 DT P "O5'" sing N N 239 DT OP2 HOP2 sing N N 240 DT "O5'" "C5'" sing N N 241 DT "C5'" "C4'" sing N N 242 DT "C5'" "H5'" sing N N 243 DT "C5'" "H5''" sing N N 244 DT "C4'" "O4'" sing N N 245 DT "C4'" "C3'" sing N N 246 DT "C4'" "H4'" sing N N 247 DT "O4'" "C1'" sing N N 248 DT "C3'" "O3'" sing N N 249 DT "C3'" "C2'" sing N N 250 DT "C3'" "H3'" sing N N 251 DT "O3'" "HO3'" sing N N 252 DT "C2'" "C1'" sing N N 253 DT "C2'" "H2'" sing N N 254 DT "C2'" "H2''" sing N N 255 DT "C1'" N1 sing N N 256 DT "C1'" "H1'" sing N N 257 DT N1 C2 sing N N 258 DT N1 C6 sing N N 259 DT C2 O2 doub N N 260 DT C2 N3 sing N N 261 DT N3 C4 sing N N 262 DT N3 H3 sing N N 263 DT C4 O4 doub N N 264 DT C4 C5 sing N N 265 DT C5 C7 sing N N 266 DT C5 C6 doub N N 267 DT C7 H71 sing N N 268 DT C7 H72 sing N N 269 DT C7 H73 sing N N 270 DT C6 H6 sing N N 271 HOH O H1 sing N N 272 HOH O H2 sing N N 273 # loop_ _ndb_struct_conf_na.entry_id _ndb_struct_conf_na.feature 1FD5 'double helix' 1FD5 'b-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 DG 2 1_555 B DC 5 1_555 -0.311 -0.109 -0.081 -10.994 4.846 0.218 1 A_DG2:DC11_B A 2 ? B 11 ? 19 1 1 A DT 3 1_555 B DA 4 1_555 0.096 -0.107 0.189 -1.294 -1.748 2.890 2 A_DT3:DA10_B A 3 ? B 10 ? 20 1 1 A DA 4 1_555 B DT 3 1_555 0.105 -0.090 -0.045 -0.156 0.704 -2.017 3 A_DA4:DT9_B A 4 ? B 9 ? 20 1 1 A DC 5 1_555 B DG 2 1_555 0.307 -0.096 -0.067 21.847 -2.049 0.419 4 A_DC5:DG8_B A 5 ? B 8 ? 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 DG 2 1_555 B DC 5 1_555 A DT 3 1_555 B DA 4 1_555 -0.067 -0.408 3.145 -2.284 4.663 26.150 -2.045 -0.424 3.022 10.178 4.985 26.652 1 AA_DG2DT3:DA10DC11_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 -0.057 -0.490 3.182 2.792 2.258 37.246 -1.051 0.444 3.136 3.526 -4.358 37.413 2 AA_DT3DA4:DT9DA10_BB A 3 ? B 10 ? A 4 ? B 9 ? 1 A DA 4 1_555 B DT 3 1_555 A DC 5 1_555 B DG 2 1_555 0.896 -0.543 2.894 -1.882 4.412 27.033 -2.081 -2.289 2.705 9.344 3.987 27.447 3 AA_DA4DC5:DG8DT9_BB A 4 ? B 9 ? A 5 ? B 8 ? # _atom_sites.entry_id 1FD5 _atom_sites.fract_transf_matrix[1][1] 0.033802 _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] 0.018505 _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] 0.024866 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C CO MG N O P # loop_