data_5BNA # _entry.id 5BNA # _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 5BNA pdb_00005bna 10.2210/pdb5bna/pdb RCSB DDL017 ? ? WWPDB D_1000179675 ? ? # 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 1983-11-02 2 'Structure model' 1 1 2008-05-22 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-03-06 # _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' 'Database references' 5 4 'Structure model' 'Derived calculations' # 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' chem_comp_atom 2 4 'Structure model' chem_comp_bond 3 4 'Structure model' database_2 4 4 'Structure model' pdbx_struct_conn_angle 5 4 'Structure model' struct_conn 6 4 'Structure model' struct_conn_type 7 4 'Structure model' struct_site # 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' '_database_2.pdbx_DOI' 2 4 'Structure model' '_database_2.pdbx_database_accession' 3 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_asym_id' 4 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_auth_seq_id' 5 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_asym_id' 6 4 'Structure model' '_pdbx_struct_conn_angle.ptnr1_label_seq_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_asym_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 13 4 'Structure model' '_pdbx_struct_conn_angle.value' 14 4 'Structure model' '_struct_conn.conn_type_id' 15 4 'Structure model' '_struct_conn.id' 16 4 'Structure model' '_struct_conn.pdbx_dist_value' 17 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 18 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 19 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 20 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 21 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 22 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 23 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 24 4 'Structure model' '_struct_conn.ptnr1_label_seq_id' 25 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 26 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 27 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 28 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 29 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 30 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 31 4 'Structure model' '_struct_conn.ptnr2_label_seq_id' 32 4 'Structure model' '_struct_conn_type.id' 33 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 34 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 35 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 5BNA _pdbx_database_status.recvd_initial_deposition_date 1983-08-22 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site BNL _pdbx_database_status.SG_entry . _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Wing, R.M.' 1 'Pjura, P.' 2 'Drew, H.R.' 3 'Dickerson, R.E.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary 'The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G' 'EMBO J.' 3 1201 1206 1984 EMJODG UK 0261-4189 0897 ? 6539674 ? 1 'A Random-Walk Model for Helix Bending in B-DNA' Proc.Natl.Acad.Sci.USA 80 7099 7103 1983 PNASA6 US 0027-8424 0040 ? ? ? 2 'Helix Geometry and Hydration in A-DNA, B-DNA and Z-DNA' 'Cold Spring Harbor Symp.Quant.Biol.' 47 13 ? 1983 CSHSAZ US 0091-7451 0421 ? ? ? 3 'Base Sequence, Helix Geometry, Hydration and Helix Stability in B-DNA' 'Biological Macromolecules and Assemblies' 2 37 126 1985 ? US 0-471-85142-6 0879 'John Wiley and Sons, New York' ? ? 4 'Crystal Structure Analysis of a Complete Turn of B-DNA' Nature 287 755 758 1980 NATUAS UK 0028-0836 0006 ? ? ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Wing, R.M.' 1 ? primary 'Pjura, P.' 2 ? primary 'Drew, H.R.' 3 ? primary 'Dickerson, R.E.' 4 ? 1 'Dickerson, R.E.' 5 ? 1 'Kopka, M.L.' 6 ? 1 'Pjura, P.' 7 ? 2 'Dickerson, R.E.' 8 ? 2 'Drew, H.R.' 9 ? 2 'Conner, B.N.' 10 ? 2 'Kopka, M.L.' 11 ? 2 'Pjura, P.E.' 12 ? 3 'Dickerson, R.E.' 13 ? 3 'Kopka, M.L.' 14 ? 3 'Pjura, P.' 15 ? 4 'Wing, R.' 16 ? 4 'Drew, H.R.' 17 ? 4 'Takano, T.' 18 ? 4 'Broka, C.' 19 ? 4 'Tanaka, S.' 20 ? 4 'Itakura, K.' 21 ? 4 'Dickerson, R.E.' 22 ? # 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*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') ; 3663.392 2 ? ? ? ? 2 non-polymer syn 'PLATINUM TRIAMINE ION' 246.170 3 ? ? ? ? 3 water nat water 18.015 128 ? ? ? ? # _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)(DC)(DG)(DA)(DA)(DT)(DT)(DC)(DG)(DC)(DG)' _entity_poly.pdbx_seq_one_letter_code_can CGCGAATTCGCG _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 'PLATINUM TRIAMINE ION' PTN 3 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 DC n 1 4 DG n 1 5 DA n 1 6 DA n 1 7 DT n 1 8 DT n 1 9 DC n 1 10 DG n 1 11 DC n 1 12 DG n # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight DA 'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O6 P' 331.222 DC 'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O7 P' 307.197 DG 'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O7 P' 347.221 DT 'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE" ? 'C10 H15 N2 O8 P' 322.208 HOH non-polymer . WATER ? 'H2 O' 18.015 PTN non-polymer . 'PLATINUM TRIAMINE ION' ? 'H9 N3 Pt 2' 246.170 # 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 DC 3 3 3 DC C A . n A 1 4 DG 4 4 4 DG +G A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DA 6 6 6 DA A A . n A 1 7 DT 7 7 7 DT T A . n A 1 8 DT 8 8 8 DT T A . n A 1 9 DC 9 9 9 DC C A . n A 1 10 DG 10 10 10 DG +G A . n A 1 11 DC 11 11 11 DC C A . n A 1 12 DG 12 12 12 DG G A . n B 1 1 DC 1 13 13 DC C B . n B 1 2 DG 2 14 14 DG G B . n B 1 3 DC 3 15 15 DC C B . n B 1 4 DG 4 16 16 DG +G B . n B 1 5 DA 5 17 17 DA A B . n B 1 6 DA 6 18 18 DA A B . n B 1 7 DT 7 19 19 DT T B . n B 1 8 DT 8 20 20 DT T B . n B 1 9 DC 9 21 21 DC C B . n B 1 10 DG 10 22 22 DG +G B . n B 1 11 DC 11 23 23 DC C B . n B 1 12 DG 12 24 24 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 PTN 1 25 25 PTN PTN A . D 2 PTN 1 26 26 PTN PTN A . E 2 PTN 1 27 27 PTN PTN B . F 3 HOH 1 30 30 HOH HOH A . F 3 HOH 2 31 31 HOH HOH A . F 3 HOH 3 33 33 HOH HOH A . F 3 HOH 4 37 37 HOH HOH A . F 3 HOH 5 40 40 HOH HOH A . F 3 HOH 6 41 41 HOH HOH A . F 3 HOH 7 42 42 HOH HOH A . F 3 HOH 8 44 44 HOH HOH A . F 3 HOH 9 45 45 HOH HOH A . F 3 HOH 10 46 46 HOH HOH A . F 3 HOH 11 51 51 HOH HOH A . F 3 HOH 12 53 53 HOH HOH A . F 3 HOH 13 58 58 HOH HOH A . F 3 HOH 14 61 61 HOH HOH A . F 3 HOH 15 65 65 HOH HOH A . F 3 HOH 16 67 67 HOH HOH A . F 3 HOH 17 71 71 HOH HOH A . F 3 HOH 18 72 72 HOH HOH A . F 3 HOH 19 87 87 HOH HOH A . F 3 HOH 20 88 88 HOH HOH A . F 3 HOH 21 89 89 HOH HOH A . F 3 HOH 22 91 91 HOH HOH A . F 3 HOH 23 93 93 HOH HOH A . F 3 HOH 24 94 94 HOH HOH A . F 3 HOH 25 107 107 HOH HOH A . F 3 HOH 26 108 108 HOH HOH A . F 3 HOH 27 109 109 HOH HOH A . F 3 HOH 28 112 112 HOH HOH A . F 3 HOH 29 113 113 HOH HOH A . F 3 HOH 30 115 115 HOH HOH A . F 3 HOH 31 116 116 HOH HOH A . F 3 HOH 32 120 120 HOH HOH A . F 3 HOH 33 124 124 HOH HOH A . F 3 HOH 34 125 125 HOH HOH A . F 3 HOH 35 127 127 HOH HOH A . F 3 HOH 36 133 133 HOH HOH A . F 3 HOH 37 137 137 HOH HOH A . F 3 HOH 38 139 139 HOH HOH A . F 3 HOH 39 144 144 HOH HOH A . F 3 HOH 40 146 146 HOH HOH A . F 3 HOH 41 149 149 HOH HOH A . F 3 HOH 42 150 150 HOH HOH A . F 3 HOH 43 152 152 HOH HOH A . G 3 HOH 1 28 28 HOH HOH B . G 3 HOH 2 29 29 HOH HOH B . G 3 HOH 3 32 32 HOH HOH B . G 3 HOH 4 34 34 HOH HOH B . G 3 HOH 5 35 35 HOH HOH B . G 3 HOH 6 36 36 HOH HOH B . G 3 HOH 7 38 38 HOH HOH B . G 3 HOH 8 39 39 HOH HOH B . G 3 HOH 9 43 43 HOH HOH B . G 3 HOH 10 47 47 HOH HOH B . G 3 HOH 11 48 48 HOH HOH B . G 3 HOH 12 49 49 HOH HOH B . G 3 HOH 13 50 50 HOH HOH B . G 3 HOH 14 52 52 HOH HOH B . G 3 HOH 15 54 54 HOH HOH B . G 3 HOH 16 55 55 HOH HOH B . G 3 HOH 17 56 56 HOH HOH B . G 3 HOH 18 57 57 HOH HOH B . G 3 HOH 19 59 59 HOH HOH B . G 3 HOH 20 60 60 HOH HOH B . G 3 HOH 21 62 62 HOH HOH B . G 3 HOH 22 63 63 HOH HOH B . G 3 HOH 23 64 64 HOH HOH B . G 3 HOH 24 66 66 HOH HOH B . G 3 HOH 25 68 68 HOH HOH B . G 3 HOH 26 69 69 HOH HOH B . G 3 HOH 27 70 70 HOH HOH B . G 3 HOH 28 73 73 HOH HOH B . G 3 HOH 29 74 74 HOH HOH B . G 3 HOH 30 75 75 HOH HOH B . G 3 HOH 31 76 76 HOH HOH B . G 3 HOH 32 77 77 HOH HOH B . G 3 HOH 33 78 78 HOH HOH B . G 3 HOH 34 79 79 HOH HOH B . G 3 HOH 35 80 80 HOH HOH B . G 3 HOH 36 81 81 HOH HOH B . G 3 HOH 37 82 82 HOH HOH B . G 3 HOH 38 83 83 HOH HOH B . G 3 HOH 39 84 84 HOH HOH B . G 3 HOH 40 85 85 HOH HOH B . G 3 HOH 41 86 86 HOH HOH B . G 3 HOH 42 90 90 HOH HOH B . G 3 HOH 43 92 92 HOH HOH B . G 3 HOH 44 95 95 HOH HOH B . G 3 HOH 45 96 96 HOH HOH B . G 3 HOH 46 97 97 HOH HOH B . G 3 HOH 47 98 98 HOH HOH B . G 3 HOH 48 99 99 HOH HOH B . G 3 HOH 49 100 100 HOH HOH B . G 3 HOH 50 101 101 HOH HOH B . G 3 HOH 51 102 102 HOH HOH B . G 3 HOH 52 103 103 HOH HOH B . G 3 HOH 53 104 104 HOH HOH B . G 3 HOH 54 105 105 HOH HOH B . G 3 HOH 55 106 106 HOH HOH B . G 3 HOH 56 110 110 HOH HOH B . G 3 HOH 57 111 111 HOH HOH B . G 3 HOH 58 114 114 HOH HOH B . G 3 HOH 59 117 117 HOH HOH B . G 3 HOH 60 118 118 HOH HOH B . G 3 HOH 61 119 119 HOH HOH B . G 3 HOH 62 121 121 HOH HOH B . G 3 HOH 63 122 122 HOH HOH B . G 3 HOH 64 123 123 HOH HOH B . G 3 HOH 65 126 126 HOH HOH B . G 3 HOH 66 128 128 HOH HOH B . G 3 HOH 67 129 129 HOH HOH B . G 3 HOH 68 130 130 HOH HOH B . G 3 HOH 69 131 131 HOH HOH B . G 3 HOH 70 132 132 HOH HOH B . G 3 HOH 71 134 134 HOH HOH B . G 3 HOH 72 135 135 HOH HOH B . G 3 HOH 73 136 136 HOH HOH B . G 3 HOH 74 138 138 HOH HOH B . G 3 HOH 75 140 140 HOH HOH B . G 3 HOH 76 141 141 HOH HOH B . G 3 HOH 77 142 142 HOH HOH B . G 3 HOH 78 143 143 HOH HOH B . G 3 HOH 79 145 145 HOH HOH B . G 3 HOH 80 147 147 HOH HOH B . G 3 HOH 81 148 148 HOH HOH B . G 3 HOH 82 151 151 HOH HOH B . G 3 HOH 83 153 153 HOH HOH B . G 3 HOH 84 154 154 HOH HOH B . G 3 HOH 85 155 155 HOH HOH B . # _software.name JACK-LEVITT _software.classification refinement _software.version . _software.citation_id ? _software.pdbx_ordinal 1 # _cell.entry_id 5BNA _cell.length_a 24.160 _cell.length_b 39.930 _cell.length_c 66.120 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5BNA _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 # _exptl.entry_id 5BNA _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_percent_sol 43.49 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.temp 277.00 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'VAPOR DIFFUSION, temperature 277.00K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _exptl_crystal_grow_comp.crystal_id _exptl_crystal_grow_comp.id _exptl_crystal_grow_comp.sol_id _exptl_crystal_grow_comp.name _exptl_crystal_grow_comp.volume _exptl_crystal_grow_comp.conc _exptl_crystal_grow_comp.details 1 1 1 WATER ? ? ? 1 2 1 MPD ? ? ? # _reflns.entry_id 5BNA _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low ? _reflns.d_resolution_high 2.600 _reflns.number_obs 2088 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _refine.entry_id 5BNA _refine.ls_number_reflns_obs 725 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 2.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 8.000 _refine.ls_d_res_high 2.600 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.1020000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _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 ? _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 ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _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 486 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 128 _refine_hist.number_atoms_total 626 _refine_hist.d_res_high 2.600 _refine_hist.d_res_low 8.000 # _database_PDB_matrix.entry_id 5BNA _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 5BNA _struct.title 'THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-G-C-G-A-A-T-T-C-G-C-G' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 5BNA _struct_keywords.pdbx_keywords DNA _struct_keywords.text 'B-DNA, DOUBLE HELIX, COMPLEXED WITH DRUG, MODIFIED, 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 2 ? E N N 2 ? F N N 3 ? G N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 5BNA _struct_ref.pdbx_db_accession 5BNA _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 5BNA A 1 ? 12 ? 5BNA 1 ? 12 ? 1 12 2 1 5BNA B 1 ? 12 ? 5BNA 13 ? 24 ? 13 24 # _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 # _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 # _struct_biol.id 1 # 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 none ? C PTN . N2 ? ? ? 1_555 B DG 4 O6 ? ? A PTN 25 B DG 16 1_555 ? ? ? ? ? ? ? 1.824 ? ? metalc1 metalc ? ? A DG 4 N7 ? ? ? 1_555 D PTN . PT ? ? A DG 4 A PTN 26 1_555 ? ? ? ? ? ? ? 2.315 ? ? metalc2 metalc ? ? A DG 10 N7 ? ? ? 1_555 E PTN . PT ? ? A DG 10 B PTN 27 1_555 ? ? ? ? ? ? ? 2.232 ? ? metalc3 metalc ? ? C PTN . PT ? ? ? 1_555 B DG 4 N7 ? ? A PTN 25 B DG 16 1_555 ? ? ? ? ? ? ? 2.164 ? ? hydrog1 hydrog ? ? A DC 1 N3 ? ? ? 1_555 B DG 12 N1 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A DC 1 N4 ? ? ? 1_555 B DG 12 O6 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A DC 1 O2 ? ? ? 1_555 B DG 12 N2 ? ? A DC 1 B DG 24 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A DG 2 N1 ? ? ? 1_555 B DC 11 N3 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A DG 2 N2 ? ? ? 1_555 B DC 11 O2 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A DG 2 O6 ? ? ? 1_555 B DC 11 N4 ? ? A DG 2 B DC 23 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A DC 3 N3 ? ? ? 1_555 B DG 10 N1 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A DC 3 N4 ? ? ? 1_555 B DG 10 O6 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A DC 3 O2 ? ? ? 1_555 B DG 10 N2 ? ? A DC 3 B DG 22 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DG 4 N1 ? ? ? 1_555 B DC 9 N3 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DG 4 N2 ? ? ? 1_555 B DC 9 O2 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DG 4 O6 ? ? ? 1_555 B DC 9 N4 ? ? A DG 4 B DC 21 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 8 N3 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 8 O4 ? ? A DA 5 B DT 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DA 6 N1 ? ? ? 1_555 B DT 7 N3 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 6 N6 ? ? ? 1_555 B DT 7 O4 ? ? A DA 6 B DT 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DT 7 N3 ? ? ? 1_555 B DA 6 N1 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DT 7 O4 ? ? ? 1_555 B DA 6 N6 ? ? A DT 7 B DA 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DT 8 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DT 8 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 8 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DC 9 N3 ? ? ? 1_555 B DG 4 N1 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DC 9 N4 ? ? ? 1_555 B DG 4 O6 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DC 9 O2 ? ? ? 1_555 B DG 4 N2 ? ? A DC 9 B DG 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DG 10 N1 ? ? ? 1_555 B DC 3 N3 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DG 10 N2 ? ? ? 1_555 B DC 3 O2 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DG 10 O6 ? ? ? 1_555 B DC 3 N4 ? ? A DG 10 B DC 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog27 hydrog ? ? A DC 11 N3 ? ? ? 1_555 B DG 2 N1 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog28 hydrog ? ? A DC 11 N4 ? ? ? 1_555 B DG 2 O6 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog29 hydrog ? ? A DC 11 O2 ? ? ? 1_555 B DG 2 N2 ? ? A DC 11 B DG 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog30 hydrog ? ? A DG 12 N1 ? ? ? 1_555 B DC 1 N3 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog31 hydrog ? ? A DG 12 N2 ? ? ? 1_555 B DC 1 O2 ? ? A DG 12 B DC 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog32 hydrog ? ? A DG 12 O6 ? ? ? 1_555 B DC 1 N4 ? ? A DG 12 B DC 13 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 N7 ? A DG 4 ? A DG 4 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N1 ? D PTN . ? A PTN 26 ? 1_555 79.0 ? 2 N7 ? A DG 4 ? A DG 4 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N2 ? D PTN . ? A PTN 26 ? 1_555 102.0 ? 3 N1 ? D PTN . ? A PTN 26 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N2 ? D PTN . ? A PTN 26 ? 1_555 175.1 ? 4 N7 ? A DG 4 ? A DG 4 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N3 ? D PTN . ? A PTN 26 ? 1_555 159.9 ? 5 N1 ? D PTN . ? A PTN 26 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N3 ? D PTN . ? A PTN 26 ? 1_555 95.5 ? 6 N2 ? D PTN . ? A PTN 26 ? 1_555 PT ? D PTN . ? A PTN 26 ? 1_555 N3 ? D PTN . ? A PTN 26 ? 1_555 85.1 ? 7 N7 ? A DG 10 ? A DG 10 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N1 ? E PTN . ? B PTN 27 ? 1_555 103.7 ? 8 N7 ? A DG 10 ? A DG 10 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N2 ? E PTN . ? B PTN 27 ? 1_555 69.7 ? 9 N1 ? E PTN . ? B PTN 27 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N2 ? E PTN . ? B PTN 27 ? 1_555 173.4 ? 10 N7 ? A DG 10 ? A DG 10 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N3 ? E PTN . ? B PTN 27 ? 1_555 144.8 ? 11 N1 ? E PTN . ? B PTN 27 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N3 ? E PTN . ? B PTN 27 ? 1_555 104.7 ? 12 N2 ? E PTN . ? B PTN 27 ? 1_555 PT ? E PTN . ? B PTN 27 ? 1_555 N3 ? E PTN . ? B PTN 27 ? 1_555 81.3 ? 13 N7 ? B DG 4 ? B DG 16 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N1 ? C PTN . ? A PTN 25 ? 1_555 105.6 ? 14 N7 ? B DG 4 ? B DG 16 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N2 ? C PTN . ? A PTN 25 ? 1_555 70.1 ? 15 N1 ? C PTN . ? A PTN 25 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N2 ? C PTN . ? A PTN 25 ? 1_555 166.3 ? 16 N7 ? B DG 4 ? B DG 16 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N3 ? C PTN . ? A PTN 25 ? 1_555 139.1 ? 17 N1 ? C PTN . ? A PTN 25 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N3 ? C PTN . ? A PTN 25 ? 1_555 98.5 ? 18 N2 ? C PTN . ? A PTN 25 ? 1_555 PT ? C PTN . ? A PTN 25 ? 1_555 N3 ? C PTN . ? A PTN 25 ? 1_555 78.7 ? # 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 A PTN 25 ? 6 'BINDING SITE FOR RESIDUE PTN A 25' AC2 Software A PTN 26 ? 2 'BINDING SITE FOR RESIDUE PTN A 26' AC3 Software B PTN 27 ? 2 'BINDING SITE FOR RESIDUE PTN B 27' 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 HOH F . ? HOH A 33 . ? 1_555 ? 2 AC1 6 HOH F . ? HOH A 71 . ? 1_555 ? 3 AC1 6 HOH F . ? HOH A 137 . ? 1_555 ? 4 AC1 6 DC B 3 ? DC B 15 . ? 1_555 ? 5 AC1 6 DG B 4 ? DG B 16 . ? 1_555 ? 6 AC1 6 HOH G . ? HOH B 57 . ? 1_555 ? 7 AC2 2 DC A 3 ? DC A 3 . ? 1_555 ? 8 AC2 2 DG A 4 ? DG A 4 . ? 1_555 ? 9 AC3 2 DG A 10 ? DG A 10 . ? 1_555 ? 10 AC3 2 DG B 2 ? DG B 14 . ? 1_555 ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 C8 A DG 2 ? ? O A HOH 89 ? ? 1.91 2 1 OP1 A DT 8 ? ? O A HOH 127 ? ? 1.95 3 1 OP2 B DT 19 ? ? O B HOH 79 ? ? 1.96 4 1 O B HOH 76 ? ? O B HOH 119 ? ? 2.02 5 1 OP2 B DG 16 ? ? O B HOH 57 ? ? 2.06 6 1 OP2 B DG 24 ? ? O B HOH 29 ? ? 2.09 7 1 OP2 A DG 10 ? ? O A HOH 61 ? ? 2.11 8 1 OP2 B DA 17 ? ? O B HOH 122 ? ? 2.18 9 1 OP2 B DC 23 ? ? O B HOH 103 ? ? 2.19 # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OP1 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 DA _pdbx_validate_symm_contact.auth_seq_id_1 5 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 O _pdbx_validate_symm_contact.auth_asym_id_2 B _pdbx_validate_symm_contact.auth_comp_id_2 HOH _pdbx_validate_symm_contact.auth_seq_id_2 39 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_745 _pdbx_validate_symm_contact.dist 2.10 # loop_ _pdbx_validate_rmsd_bond.id _pdbx_validate_rmsd_bond.PDB_model_num _pdbx_validate_rmsd_bond.auth_atom_id_1 _pdbx_validate_rmsd_bond.auth_asym_id_1 _pdbx_validate_rmsd_bond.auth_comp_id_1 _pdbx_validate_rmsd_bond.auth_seq_id_1 _pdbx_validate_rmsd_bond.PDB_ins_code_1 _pdbx_validate_rmsd_bond.label_alt_id_1 _pdbx_validate_rmsd_bond.auth_atom_id_2 _pdbx_validate_rmsd_bond.auth_asym_id_2 _pdbx_validate_rmsd_bond.auth_comp_id_2 _pdbx_validate_rmsd_bond.auth_seq_id_2 _pdbx_validate_rmsd_bond.PDB_ins_code_2 _pdbx_validate_rmsd_bond.label_alt_id_2 _pdbx_validate_rmsd_bond.bond_value _pdbx_validate_rmsd_bond.bond_target_value _pdbx_validate_rmsd_bond.bond_deviation _pdbx_validate_rmsd_bond.bond_standard_deviation _pdbx_validate_rmsd_bond.linker_flag 1 1 C5 A DC 1 ? ? C6 A DC 1 ? ? 1.410 1.339 0.071 0.008 N 2 1 "O3'" A DG 2 ? ? "C3'" A DG 2 ? ? 1.374 1.419 -0.045 0.006 N 3 1 N3 A DG 2 ? ? C4 A DG 2 ? ? 1.396 1.350 0.046 0.007 N 4 1 C5 A DG 2 ? ? N7 A DG 2 ? ? 1.341 1.388 -0.047 0.006 N 5 1 N7 A DG 2 ? ? C8 A DG 2 ? ? 1.362 1.305 0.057 0.006 N 6 1 N7 A DG 4 ? ? C8 A DG 4 ? ? 1.342 1.305 0.037 0.006 N 7 1 N3 A DA 5 ? ? C4 A DA 5 ? ? 1.401 1.344 0.057 0.006 N 8 1 C5 A DA 5 ? ? C6 A DA 5 ? ? 1.465 1.406 0.059 0.009 N 9 1 C5 A DA 5 ? ? N7 A DA 5 ? ? 1.347 1.388 -0.041 0.006 N 10 1 "O3'" A DA 6 ? ? "C3'" A DA 6 ? ? 1.383 1.419 -0.036 0.006 N 11 1 N3 A DA 6 ? ? C4 A DA 6 ? ? 1.399 1.344 0.055 0.006 N 12 1 C5 A DA 6 ? ? N7 A DA 6 ? ? 1.328 1.388 -0.060 0.006 N 13 1 C5 A DT 7 ? ? C6 A DT 7 ? ? 1.383 1.339 0.044 0.007 N 14 1 "O3'" A DT 8 ? ? "C3'" A DT 8 ? ? 1.353 1.419 -0.066 0.006 N 15 1 C5 A DT 8 ? ? C6 A DT 8 ? ? 1.409 1.339 0.070 0.007 N 16 1 C5 A DT 8 ? ? C7 A DT 8 ? ? 1.545 1.496 0.049 0.006 N 17 1 C5 A DC 9 ? ? C6 A DC 9 ? ? 1.394 1.339 0.055 0.008 N 18 1 N3 A DG 10 ? ? C4 A DG 10 ? ? 1.422 1.350 0.072 0.007 N 19 1 N7 A DG 10 ? ? C8 A DG 10 ? ? 1.353 1.305 0.048 0.006 N 20 1 C5 A DC 11 ? ? C6 A DC 11 ? ? 1.407 1.339 0.068 0.008 N 21 1 N3 A DG 12 ? ? C4 A DG 12 ? ? 1.422 1.350 0.072 0.007 N 22 1 N7 A DG 12 ? ? C8 A DG 12 ? ? 1.345 1.305 0.040 0.006 N 23 1 C5 B DC 13 ? ? C6 B DC 13 ? ? 1.408 1.339 0.069 0.008 N 24 1 N3 B DG 14 ? ? C4 B DG 14 ? ? 1.420 1.350 0.070 0.007 N 25 1 C5 B DG 14 ? ? N7 B DG 14 ? ? 1.349 1.388 -0.039 0.006 N 26 1 C5 B DC 15 ? ? C6 B DC 15 ? ? 1.410 1.339 0.071 0.008 N 27 1 C5 B DG 16 ? ? C6 B DG 16 ? ? 1.482 1.419 0.063 0.010 N 28 1 N3 B DA 17 ? ? C4 B DA 17 ? ? 1.384 1.344 0.040 0.006 N 29 1 N3 B DA 18 ? ? C4 B DA 18 ? ? 1.398 1.344 0.054 0.006 N 30 1 C5 B DA 18 ? ? N7 B DA 18 ? ? 1.339 1.388 -0.049 0.006 N 31 1 C5 B DT 19 ? ? C6 B DT 19 ? ? 1.410 1.339 0.071 0.007 N 32 1 C5 B DT 20 ? ? C6 B DT 20 ? ? 1.398 1.339 0.059 0.007 N 33 1 C4 B DC 21 ? ? N4 B DC 21 ? ? 1.391 1.335 0.056 0.009 N 34 1 N3 B DC 21 ? ? C4 B DC 21 ? ? 1.383 1.335 0.048 0.007 N 35 1 C5 B DG 22 ? ? N7 B DG 22 ? ? 1.345 1.388 -0.043 0.006 N 36 1 N7 B DG 22 ? ? C8 B DG 22 ? ? 1.352 1.305 0.047 0.006 N 37 1 C5 B DC 23 ? ? C6 B DC 23 ? ? 1.409 1.339 0.070 0.008 N 38 1 C5 B DG 24 ? ? N7 B DG 24 ? ? 1.331 1.388 -0.057 0.006 N 39 1 N7 B DG 24 ? ? C8 B DG 24 ? ? 1.352 1.305 0.047 0.006 N # 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 "C5'" A DC 1 ? ? "C4'" A DC 1 ? ? "O4'" A DC 1 ? ? 121.14 109.80 11.34 1.10 N 2 1 "O4'" A DC 1 ? ? "C1'" A DC 1 ? ? N1 A DC 1 ? ? 111.52 108.30 3.22 0.30 N 3 1 "O5'" A DG 2 ? ? "C5'" A DG 2 ? ? "C4'" A DG 2 ? ? 103.16 109.40 -6.24 0.80 N 4 1 C2 A DG 2 ? ? N3 A DG 2 ? ? C4 A DG 2 ? ? 115.73 111.90 3.83 0.50 N 5 1 N3 A DG 2 ? ? C4 A DG 2 ? ? C5 A DG 2 ? ? 125.23 128.60 -3.37 0.50 N 6 1 "O4'" A DC 3 ? ? "C1'" A DC 3 ? ? N1 A DC 3 ? ? 102.89 108.00 -5.11 0.70 N 7 1 "O5'" A DG 4 ? ? "C5'" A DG 4 ? ? "C4'" A DG 4 ? ? 104.52 109.40 -4.88 0.80 N 8 1 C2 A DG 4 ? ? N3 A DG 4 ? ? C4 A DG 4 ? ? 116.74 111.90 4.84 0.50 N 9 1 C8 A DA 5 ? ? N9 A DA 5 ? ? C4 A DA 5 ? ? 103.19 105.80 -2.61 0.40 N 10 1 "O3'" A DA 5 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 119.24 110.50 8.74 1.10 Y 11 1 OP1 A DA 6 ? ? P A DA 6 ? ? OP2 A DA 6 ? ? 110.40 119.60 -9.20 1.50 N 12 1 "O5'" A DA 6 ? ? "C5'" A DA 6 ? ? "C4'" A DA 6 ? ? 104.16 109.40 -5.24 0.80 N 13 1 "O4'" A DA 6 ? ? "C1'" A DA 6 ? ? N9 A DA 6 ? ? 114.04 108.30 5.74 0.30 N 14 1 "O5'" A DT 7 ? ? "C5'" A DT 7 ? ? "C4'" A DT 7 ? ? 104.05 109.40 -5.35 0.80 N 15 1 C2 A DT 7 ? ? N3 A DT 7 ? ? C4 A DT 7 ? ? 122.85 127.20 -4.35 0.60 N 16 1 N3 A DT 7 ? ? C4 A DT 7 ? ? C5 A DT 7 ? ? 118.86 115.20 3.66 0.60 N 17 1 C6 A DT 7 ? ? C5 A DT 7 ? ? C7 A DT 7 ? ? 118.51 122.90 -4.39 0.60 N 18 1 "O5'" A DT 8 ? ? "C5'" A DT 8 ? ? "C4'" A DT 8 ? ? 104.00 109.40 -5.40 0.80 N 19 1 C2 A DT 8 ? ? N3 A DT 8 ? ? C4 A DT 8 ? ? 123.01 127.20 -4.19 0.60 N 20 1 N3 A DT 8 ? ? C4 A DT 8 ? ? C5 A DT 8 ? ? 119.38 115.20 4.18 0.60 N 21 1 N3 A DT 8 ? ? C2 A DT 8 ? ? O2 A DT 8 ? ? 118.44 122.30 -3.86 0.60 N 22 1 N3 A DT 8 ? ? C4 A DT 8 ? ? O4 A DT 8 ? ? 114.30 119.90 -5.60 0.60 N 23 1 C4 A DT 8 ? ? C5 A DT 8 ? ? C7 A DT 8 ? ? 122.74 119.00 3.74 0.60 N 24 1 "O5'" A DC 9 ? ? "C5'" A DC 9 ? ? "C4'" A DC 9 ? ? 101.95 109.40 -7.45 0.80 N 25 1 "C3'" A DG 10 ? ? "C2'" A DG 10 ? ? "C1'" A DG 10 ? ? 97.30 102.40 -5.10 0.80 N 26 1 "O4'" A DG 10 ? ? "C1'" A DG 10 ? ? N9 A DG 10 ? ? 111.97 108.30 3.67 0.30 N 27 1 N3 A DG 10 ? ? C4 A DG 10 ? ? C5 A DG 10 ? ? 125.40 128.60 -3.20 0.50 N 28 1 "O4'" A DC 11 ? ? "C1'" A DC 11 ? ? N1 A DC 11 ? ? 111.39 108.30 3.09 0.30 N 29 1 "C5'" A DG 12 ? ? "C4'" A DG 12 ? ? "C3'" A DG 12 ? ? 123.43 115.70 7.73 1.20 N 30 1 C2 A DG 12 ? ? N3 A DG 12 ? ? C4 A DG 12 ? ? 115.08 111.90 3.18 0.50 N 31 1 "C5'" B DC 13 ? ? "C4'" B DC 13 ? ? "O4'" B DC 13 ? ? 120.61 109.80 10.81 1.10 N 32 1 "O4'" B DC 13 ? ? "C1'" B DC 13 ? ? N1 B DC 13 ? ? 118.60 108.30 10.30 0.30 N 33 1 C2 B DG 14 ? ? N3 B DG 14 ? ? C4 B DG 14 ? ? 115.31 111.90 3.41 0.50 N 34 1 N3 B DG 14 ? ? C4 B DG 14 ? ? C5 B DG 14 ? ? 124.93 128.60 -3.67 0.50 N 35 1 N3 B DG 14 ? ? C4 B DG 14 ? ? N9 B DG 14 ? ? 129.88 126.00 3.88 0.60 N 36 1 C5 B DG 14 ? ? C6 B DG 14 ? ? O6 B DG 14 ? ? 124.83 128.60 -3.77 0.60 N 37 1 "O5'" B DC 15 ? ? "C5'" B DC 15 ? ? "C4'" B DC 15 ? ? 103.14 109.40 -6.26 0.80 N 38 1 C2 B DG 16 ? ? N3 B DG 16 ? ? C4 B DG 16 ? ? 116.37 111.90 4.47 0.50 N 39 1 N3 B DG 16 ? ? C4 B DG 16 ? ? C5 B DG 16 ? ? 125.45 128.60 -3.15 0.50 N 40 1 OP1 B DA 17 ? ? P B DA 17 ? ? OP2 B DA 17 ? ? 107.69 119.60 -11.91 1.50 N 41 1 "C5'" B DA 17 ? ? "C4'" B DA 17 ? ? "O4'" B DA 17 ? ? 118.39 109.80 8.59 1.10 N 42 1 "O4'" B DA 17 ? ? "C1'" B DA 17 ? ? N9 B DA 17 ? ? 111.22 108.30 2.92 0.30 N 43 1 "O5'" B DA 18 ? ? "C5'" B DA 18 ? ? "C4'" B DA 18 ? ? 103.54 109.40 -5.86 0.80 N 44 1 "O4'" B DT 19 ? ? "C1'" B DT 19 ? ? N1 B DT 19 ? ? 111.68 108.30 3.38 0.30 N 45 1 C2 B DT 19 ? ? N3 B DT 19 ? ? C4 B DT 19 ? ? 123.37 127.20 -3.83 0.60 N 46 1 "O4'" B DT 20 ? ? "C1'" B DT 20 ? ? N1 B DT 20 ? ? 103.76 108.00 -4.24 0.70 N 47 1 C2 B DT 20 ? ? N3 B DT 20 ? ? C4 B DT 20 ? ? 123.00 127.20 -4.20 0.60 N 48 1 N3 B DT 20 ? ? C4 B DT 20 ? ? C5 B DT 20 ? ? 119.47 115.20 4.27 0.60 N 49 1 "O5'" B DC 21 ? ? "C5'" B DC 21 ? ? "C4'" B DC 21 ? ? 103.12 109.40 -6.28 0.80 N 50 1 "C1'" B DC 21 ? ? "O4'" B DC 21 ? ? "C4'" B DC 21 ? ? 103.38 110.10 -6.72 1.00 N 51 1 N3 B DC 21 ? ? C4 B DC 21 ? ? N4 B DC 21 ? ? 124.55 118.00 6.55 0.70 N 52 1 C5 B DC 21 ? ? C4 B DC 21 ? ? N4 B DC 21 ? ? 114.60 120.20 -5.60 0.70 N 53 1 "O3'" B DC 21 ? ? P B DG 22 ? ? OP2 B DG 22 ? ? 122.07 110.50 11.57 1.10 Y 54 1 "O4'" B DG 22 ? ? "C4'" B DG 22 ? ? "C3'" B DG 22 ? ? 101.64 104.50 -2.86 0.40 N 55 1 C2 B DG 22 ? ? N3 B DG 22 ? ? C4 B DG 22 ? ? 115.93 111.90 4.03 0.50 N 56 1 C8 B DG 22 ? ? N9 B DG 22 ? ? C4 B DG 22 ? ? 102.76 106.40 -3.64 0.40 N 57 1 N9 B DG 22 ? ? C4 B DG 22 ? ? C5 B DG 22 ? ? 108.54 105.40 3.14 0.40 N 58 1 "O4'" B DC 23 ? ? "C1'" B DC 23 ? ? N1 B DC 23 ? ? 112.09 108.30 3.79 0.30 N 59 1 C2 B DC 23 ? ? N3 B DC 23 ? ? C4 B DC 23 ? ? 123.40 119.90 3.50 0.50 N 60 1 N1 B DC 23 ? ? C2 B DC 23 ? ? O2 B DC 23 ? ? 122.50 118.90 3.60 0.60 N 61 1 "C4'" B DG 24 ? ? "C3'" B DG 24 ? ? "C2'" B DG 24 ? ? 95.51 102.20 -6.69 0.70 N 62 1 C2 B DG 24 ? ? N3 B DG 24 ? ? C4 B DG 24 ? ? 116.40 111.90 4.50 0.50 N 63 1 N3 B DG 24 ? ? C4 B DG 24 ? ? C5 B DG 24 ? ? 124.74 128.60 -3.86 0.50 N 64 1 C8 B DG 24 ? ? N9 B DG 24 ? ? C4 B DG 24 ? ? 102.79 106.40 -3.61 0.40 N 65 1 N9 B DG 24 ? ? C4 B DG 24 ? ? C5 B DG 24 ? ? 109.10 105.40 3.70 0.40 N 66 1 N1 B DG 24 ? ? C6 B DG 24 ? ? O6 B DG 24 ? ? 115.76 119.90 -4.14 0.60 N # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id "C1'" _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id B _pdbx_validate_chiral.auth_comp_id DT _pdbx_validate_chiral.auth_seq_id 19 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details 'WRONG HAND' _pdbx_validate_chiral.omega . # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 DG A 2 ? ? 0.089 'SIDE CHAIN' 2 1 DT A 8 ? ? 0.071 'SIDE CHAIN' 3 1 DG A 12 ? ? 0.077 'SIDE CHAIN' 4 1 DG B 14 ? ? 0.063 'SIDE CHAIN' 5 1 DC B 15 ? ? 0.082 'SIDE CHAIN' 6 1 DG B 16 ? ? 0.137 'SIDE CHAIN' 7 1 DA B 17 ? ? 0.086 'SIDE CHAIN' 8 1 DC B 23 ? ? 0.094 'SIDE CHAIN' # _struct_site_keywords.site_id 1 _struct_site_keywords.text 'OUTSIDE BINDER' # loop_ _refine_B_iso.class _refine_B_iso.details _refine_B_iso.treatment _refine_B_iso.pdbx_refine_id 'ALL ATOMS' TR isotropic 'X-RAY DIFFRACTION' 'ALL PT ATOMS' TR anisotropic 'X-RAY DIFFRACTION' 'ALL WATERS' TR isotropic 'X-RAY DIFFRACTION' # loop_ _refine_occupancy.class _refine_occupancy.treatment _refine_occupancy.pdbx_refine_id 'ALL ATOMS' fix 'X-RAY DIFFRACTION' 'ALL PT ATOMS' fix 'X-RAY DIFFRACTION' 'ALL WATERS' fix 'X-RAY DIFFRACTION' # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal DA OP3 O N N 1 DA P P N N 2 DA OP1 O N N 3 DA OP2 O N N 4 DA "O5'" O N N 5 DA "C5'" C N N 6 DA "C4'" C N R 7 DA "O4'" O N N 8 DA "C3'" C N S 9 DA "O3'" O N N 10 DA "C2'" C N N 11 DA "C1'" C N R 12 DA N9 N Y N 13 DA C8 C Y N 14 DA N7 N Y N 15 DA C5 C Y N 16 DA C6 C Y N 17 DA N6 N N N 18 DA N1 N Y N 19 DA C2 C Y N 20 DA N3 N Y N 21 DA C4 C Y N 22 DA HOP3 H N N 23 DA HOP2 H N N 24 DA "H5'" H N N 25 DA "H5''" H N N 26 DA "H4'" H N N 27 DA "H3'" H N N 28 DA "HO3'" H N N 29 DA "H2'" H N N 30 DA "H2''" H N N 31 DA "H1'" H N N 32 DA H8 H N N 33 DA H61 H N N 34 DA H62 H N N 35 DA H2 H N N 36 DC OP3 O N N 37 DC P P N N 38 DC OP1 O N N 39 DC OP2 O N N 40 DC "O5'" O N N 41 DC "C5'" C N N 42 DC "C4'" C N R 43 DC "O4'" O N N 44 DC "C3'" C N S 45 DC "O3'" O N N 46 DC "C2'" C N N 47 DC "C1'" C N R 48 DC N1 N N N 49 DC C2 C N N 50 DC O2 O N N 51 DC N3 N N N 52 DC C4 C N N 53 DC N4 N N N 54 DC C5 C N N 55 DC C6 C N N 56 DC HOP3 H N N 57 DC HOP2 H N N 58 DC "H5'" H N N 59 DC "H5''" H N N 60 DC "H4'" H N N 61 DC "H3'" H N N 62 DC "HO3'" H N N 63 DC "H2'" H N N 64 DC "H2''" H N N 65 DC "H1'" H N N 66 DC H41 H N N 67 DC H42 H N N 68 DC H5 H N N 69 DC H6 H N N 70 DG OP3 O N N 71 DG P P N N 72 DG OP1 O N N 73 DG OP2 O N N 74 DG "O5'" O N N 75 DG "C5'" C N N 76 DG "C4'" C N R 77 DG "O4'" O N N 78 DG "C3'" C N S 79 DG "O3'" O N N 80 DG "C2'" C N N 81 DG "C1'" C N R 82 DG N9 N Y N 83 DG C8 C Y N 84 DG N7 N Y N 85 DG C5 C Y N 86 DG C6 C N N 87 DG O6 O N N 88 DG N1 N N N 89 DG C2 C N N 90 DG N2 N N N 91 DG N3 N N N 92 DG C4 C Y N 93 DG HOP3 H N N 94 DG HOP2 H N N 95 DG "H5'" H N N 96 DG "H5''" H N N 97 DG "H4'" H N N 98 DG "H3'" H N N 99 DG "HO3'" H N N 100 DG "H2'" H N N 101 DG "H2''" H N N 102 DG "H1'" H N N 103 DG H8 H N N 104 DG H1 H N N 105 DG H21 H N N 106 DG H22 H N N 107 DT OP3 O N N 108 DT P P N N 109 DT OP1 O N N 110 DT OP2 O N N 111 DT "O5'" O N N 112 DT "C5'" C N N 113 DT "C4'" C N R 114 DT "O4'" O N N 115 DT "C3'" C N S 116 DT "O3'" O N N 117 DT "C2'" C N N 118 DT "C1'" C N R 119 DT N1 N N N 120 DT C2 C N N 121 DT O2 O N N 122 DT N3 N N N 123 DT C4 C N N 124 DT O4 O N N 125 DT C5 C N N 126 DT C7 C N N 127 DT C6 C N N 128 DT HOP3 H N N 129 DT HOP2 H N N 130 DT "H5'" H N N 131 DT "H5''" H N N 132 DT "H4'" H N N 133 DT "H3'" H N N 134 DT "HO3'" H N N 135 DT "H2'" H N N 136 DT "H2''" H N N 137 DT "H1'" H N N 138 DT H3 H N N 139 DT H71 H N N 140 DT H72 H N N 141 DT H73 H N N 142 DT H6 H N N 143 HOH O O N N 144 HOH H1 H N N 145 HOH H2 H N N 146 PTN PT PT N N 147 PTN N1 N N N 148 PTN N2 N N N 149 PTN N3 N N N 150 PTN H11 H N N 151 PTN H12 H N N 152 PTN H13 H N N 153 PTN H21 H N N 154 PTN H22 H N N 155 PTN H23 H N N 156 PTN H31 H N N 157 PTN H32 H N N 158 PTN H33 H N N 159 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal DA OP3 P sing N N 1 DA OP3 HOP3 sing N N 2 DA P OP1 doub N N 3 DA P OP2 sing N N 4 DA P "O5'" sing N N 5 DA OP2 HOP2 sing N N 6 DA "O5'" "C5'" sing N N 7 DA "C5'" "C4'" sing N N 8 DA "C5'" "H5'" sing N N 9 DA "C5'" "H5''" sing N N 10 DA "C4'" "O4'" sing N N 11 DA "C4'" "C3'" sing N N 12 DA "C4'" "H4'" sing N N 13 DA "O4'" "C1'" sing N N 14 DA "C3'" "O3'" sing N N 15 DA "C3'" "C2'" sing N N 16 DA "C3'" "H3'" sing N N 17 DA "O3'" "HO3'" sing N N 18 DA "C2'" "C1'" sing N N 19 DA "C2'" "H2'" sing N N 20 DA "C2'" "H2''" sing N N 21 DA "C1'" N9 sing N N 22 DA "C1'" "H1'" sing N N 23 DA N9 C8 sing Y N 24 DA N9 C4 sing Y N 25 DA C8 N7 doub Y N 26 DA C8 H8 sing N N 27 DA N7 C5 sing Y N 28 DA C5 C6 sing Y N 29 DA C5 C4 doub Y N 30 DA C6 N6 sing N N 31 DA C6 N1 doub Y N 32 DA N6 H61 sing N N 33 DA N6 H62 sing N N 34 DA N1 C2 sing Y N 35 DA C2 N3 doub Y N 36 DA C2 H2 sing N N 37 DA N3 C4 sing Y N 38 DC OP3 P sing N N 39 DC OP3 HOP3 sing N N 40 DC P OP1 doub N N 41 DC P OP2 sing N N 42 DC P "O5'" sing N N 43 DC OP2 HOP2 sing N N 44 DC "O5'" "C5'" sing N N 45 DC "C5'" "C4'" sing N N 46 DC "C5'" "H5'" sing N N 47 DC "C5'" "H5''" sing N N 48 DC "C4'" "O4'" sing N N 49 DC "C4'" "C3'" sing N N 50 DC "C4'" "H4'" sing N N 51 DC "O4'" "C1'" sing N N 52 DC "C3'" "O3'" sing N N 53 DC "C3'" "C2'" sing N N 54 DC "C3'" "H3'" sing N N 55 DC "O3'" "HO3'" sing N N 56 DC "C2'" "C1'" sing N N 57 DC "C2'" "H2'" sing N N 58 DC "C2'" "H2''" sing N N 59 DC "C1'" N1 sing N N 60 DC "C1'" "H1'" sing N N 61 DC N1 C2 sing N N 62 DC N1 C6 sing N N 63 DC C2 O2 doub N N 64 DC C2 N3 sing N N 65 DC N3 C4 doub N N 66 DC C4 N4 sing N N 67 DC C4 C5 sing N N 68 DC N4 H41 sing N N 69 DC N4 H42 sing N N 70 DC C5 C6 doub N N 71 DC C5 H5 sing N N 72 DC C6 H6 sing N N 73 DG OP3 P sing N N 74 DG OP3 HOP3 sing N N 75 DG P OP1 doub N N 76 DG P OP2 sing N N 77 DG P "O5'" sing N N 78 DG OP2 HOP2 sing N N 79 DG "O5'" "C5'" sing N N 80 DG "C5'" "C4'" sing N N 81 DG "C5'" "H5'" sing N N 82 DG "C5'" "H5''" sing N N 83 DG "C4'" "O4'" sing N N 84 DG "C4'" "C3'" sing N N 85 DG "C4'" "H4'" sing N N 86 DG "O4'" "C1'" sing N N 87 DG "C3'" "O3'" sing N N 88 DG "C3'" "C2'" sing N N 89 DG "C3'" "H3'" sing N N 90 DG "O3'" "HO3'" sing N N 91 DG "C2'" "C1'" sing N N 92 DG "C2'" "H2'" sing N N 93 DG "C2'" "H2''" sing N N 94 DG "C1'" N9 sing N N 95 DG "C1'" "H1'" sing N N 96 DG N9 C8 sing Y N 97 DG N9 C4 sing Y N 98 DG C8 N7 doub Y N 99 DG C8 H8 sing N N 100 DG N7 C5 sing Y N 101 DG C5 C6 sing N N 102 DG C5 C4 doub Y N 103 DG C6 O6 doub N N 104 DG C6 N1 sing N N 105 DG N1 C2 sing N N 106 DG N1 H1 sing N N 107 DG C2 N2 sing N N 108 DG C2 N3 doub N N 109 DG N2 H21 sing N N 110 DG N2 H22 sing N N 111 DG N3 C4 sing N N 112 DT OP3 P sing N N 113 DT OP3 HOP3 sing N N 114 DT P OP1 doub N N 115 DT P OP2 sing N N 116 DT P "O5'" sing N N 117 DT OP2 HOP2 sing N N 118 DT "O5'" "C5'" sing N N 119 DT "C5'" "C4'" sing N N 120 DT "C5'" "H5'" sing N N 121 DT "C5'" "H5''" sing N N 122 DT "C4'" "O4'" sing N N 123 DT "C4'" "C3'" sing N N 124 DT "C4'" "H4'" sing N N 125 DT "O4'" "C1'" sing N N 126 DT "C3'" "O3'" sing N N 127 DT "C3'" "C2'" sing N N 128 DT "C3'" "H3'" sing N N 129 DT "O3'" "HO3'" sing N N 130 DT "C2'" "C1'" sing N N 131 DT "C2'" "H2'" sing N N 132 DT "C2'" "H2''" sing N N 133 DT "C1'" N1 sing N N 134 DT "C1'" "H1'" sing N N 135 DT N1 C2 sing N N 136 DT N1 C6 sing N N 137 DT C2 O2 doub N N 138 DT C2 N3 sing N N 139 DT N3 C4 sing N N 140 DT N3 H3 sing N N 141 DT C4 O4 doub N N 142 DT C4 C5 sing N N 143 DT C5 C7 sing N N 144 DT C5 C6 doub N N 145 DT C7 H71 sing N N 146 DT C7 H72 sing N N 147 DT C7 H73 sing N N 148 DT C6 H6 sing N N 149 HOH O H1 sing N N 150 HOH O H2 sing N N 151 PTN PT N1 sing N N 152 PTN PT N2 sing N N 153 PTN PT N3 sing N N 154 PTN N1 H11 sing N N 155 PTN N1 H12 sing N N 156 PTN N1 H13 sing N N 157 PTN N2 H21 sing N N 158 PTN N2 H22 sing N N 159 PTN N2 H23 sing N N 160 PTN N3 H31 sing N N 161 PTN N3 H32 sing N N 162 PTN N3 H33 sing N N 163 # _ndb_struct_conf_na.entry_id 5BNA _ndb_struct_conf_na.feature '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 DC 1 1_555 B DG 12 1_555 0.311 -0.162 0.279 -1.273 -15.589 1.581 1 A_DC1:DG24_B A 1 ? B 24 ? 19 1 1 A DG 2 1_555 B DC 11 1_555 -1.494 -0.410 -0.130 -0.586 -21.217 -5.498 2 A_DG2:DC23_B A 2 ? B 23 ? 19 1 1 A DC 3 1_555 B DG 10 1_555 -0.258 -0.200 0.338 -4.270 1.361 -1.979 3 A_DC3:DG22_B A 3 ? B 22 ? 19 1 1 A DG 4 1_555 B DC 9 1_555 0.056 -0.063 0.281 17.633 -18.130 -2.848 4 A_DG4:DC21_B A 4 ? B 21 ? 19 1 1 A DA 5 1_555 B DT 8 1_555 -0.460 -0.273 0.180 4.959 -21.151 0.090 5 A_DA5:DT20_B A 5 ? B 20 ? 20 1 1 A DA 6 1_555 B DT 7 1_555 0.068 -0.097 -0.300 -9.043 -21.098 -10.957 6 A_DA6:DT19_B A 6 ? B 19 ? 20 1 1 A DT 7 1_555 B DA 6 1_555 -0.246 -0.035 0.381 -2.002 -23.317 8.591 7 A_DT7:DA18_B A 7 ? B 18 ? 20 1 1 A DT 8 1_555 B DA 5 1_555 -0.598 -0.185 -0.482 -0.150 -25.683 6.239 8 A_DT8:DA17_B A 8 ? B 17 ? 20 1 1 A DC 9 1_555 B DG 4 1_555 -0.125 -0.190 0.280 -22.554 -10.315 -0.472 9 A_DC9:DG16_B A 9 ? B 16 ? 19 1 1 A DG 10 1_555 B DC 3 1_555 -0.652 -0.004 0.023 4.347 -2.040 0.999 10 A_DG10:DC15_B A 10 ? B 15 ? 19 1 1 A DC 11 1_555 B DG 2 1_555 -1.073 -0.262 1.077 2.208 -24.933 -12.984 11 A_DC11:DG14_B A 11 ? B 14 ? 19 1 1 A DG 12 1_555 B DC 1 1_555 -1.377 -0.110 0.193 -1.384 10.180 7.158 12 A_DG12:DC13_B A 12 ? B 13 ? 19 1 # loop_ _ndb_struct_na_base_pair_step.model_number _ndb_struct_na_base_pair_step.i_label_asym_id_1 _ndb_struct_na_base_pair_step.i_label_comp_id_1 _ndb_struct_na_base_pair_step.i_label_seq_id_1 _ndb_struct_na_base_pair_step.i_symmetry_1 _ndb_struct_na_base_pair_step.j_label_asym_id_1 _ndb_struct_na_base_pair_step.j_label_comp_id_1 _ndb_struct_na_base_pair_step.j_label_seq_id_1 _ndb_struct_na_base_pair_step.j_symmetry_1 _ndb_struct_na_base_pair_step.i_label_asym_id_2 _ndb_struct_na_base_pair_step.i_label_comp_id_2 _ndb_struct_na_base_pair_step.i_label_seq_id_2 _ndb_struct_na_base_pair_step.i_symmetry_2 _ndb_struct_na_base_pair_step.j_label_asym_id_2 _ndb_struct_na_base_pair_step.j_label_comp_id_2 _ndb_struct_na_base_pair_step.j_label_seq_id_2 _ndb_struct_na_base_pair_step.j_symmetry_2 _ndb_struct_na_base_pair_step.shift _ndb_struct_na_base_pair_step.slide _ndb_struct_na_base_pair_step.rise _ndb_struct_na_base_pair_step.tilt _ndb_struct_na_base_pair_step.roll _ndb_struct_na_base_pair_step.twist _ndb_struct_na_base_pair_step.x_displacement _ndb_struct_na_base_pair_step.y_displacement _ndb_struct_na_base_pair_step.helical_rise _ndb_struct_na_base_pair_step.inclination _ndb_struct_na_base_pair_step.tip _ndb_struct_na_base_pair_step.helical_twist _ndb_struct_na_base_pair_step.step_number _ndb_struct_na_base_pair_step.step_name _ndb_struct_na_base_pair_step.i_auth_asym_id_1 _ndb_struct_na_base_pair_step.i_auth_seq_id_1 _ndb_struct_na_base_pair_step.i_PDB_ins_code_1 _ndb_struct_na_base_pair_step.j_auth_asym_id_1 _ndb_struct_na_base_pair_step.j_auth_seq_id_1 _ndb_struct_na_base_pair_step.j_PDB_ins_code_1 _ndb_struct_na_base_pair_step.i_auth_asym_id_2 _ndb_struct_na_base_pair_step.i_auth_seq_id_2 _ndb_struct_na_base_pair_step.i_PDB_ins_code_2 _ndb_struct_na_base_pair_step.j_auth_asym_id_2 _ndb_struct_na_base_pair_step.j_auth_seq_id_2 _ndb_struct_na_base_pair_step.j_PDB_ins_code_2 1 A DC 1 1_555 B DG 12 1_555 A DG 2 1_555 B DC 11 1_555 -1.055 0.094 3.350 -1.886 6.152 28.540 -1.199 1.664 3.357 12.282 3.765 29.241 1 AA_DC1DG2:DC23DG24_BB A 1 ? B 24 ? A 2 ? B 23 ? 1 A DG 2 1_555 B DC 11 1_555 A DC 3 1_555 B DG 10 1_555 0.450 0.836 3.545 -4.994 -9.759 43.475 2.032 -1.070 3.226 -12.931 6.618 44.771 2 AA_DG2DC3:DG22DC23_BB A 2 ? B 23 ? A 3 ? B 22 ? 1 A DC 3 1_555 B DG 10 1_555 A DG 4 1_555 B DC 9 1_555 -0.297 0.613 3.122 5.241 5.577 29.643 0.096 1.563 3.087 10.679 -10.035 30.594 3 AA_DC3DG4:DC21DG22_BB A 3 ? B 22 ? A 4 ? B 21 ? 1 A DG 4 1_555 B DC 9 1_555 A DA 5 1_555 B DT 8 1_555 0.260 -0.099 3.415 -1.233 1.778 34.479 -0.453 -0.637 3.394 2.996 2.078 34.545 4 AA_DG4DA5:DT20DC21_BB A 4 ? B 21 ? A 5 ? B 20 ? 1 A DA 5 1_555 B DT 8 1_555 A DA 6 1_555 B DT 7 1_555 -0.146 -0.290 3.659 3.661 4.152 45.708 -0.769 0.537 3.599 5.323 -4.692 46.024 5 AA_DA5DA6:DT19DT20_BB A 5 ? B 20 ? A 6 ? B 19 ? 1 A DA 6 1_555 B DT 7 1_555 A DT 7 1_555 B DA 6 1_555 0.441 -0.721 2.965 -2.326 0.200 26.599 -1.609 -1.500 2.911 0.434 5.043 26.699 6 AA_DA6DT7:DA18DT19_BB A 6 ? B 19 ? A 7 ? B 18 ? 1 A DT 7 1_555 B DA 6 1_555 A DT 8 1_555 B DA 5 1_555 -0.494 -0.262 3.179 6.927 2.475 31.258 -0.898 2.079 2.975 4.515 -12.637 32.091 7 AA_DT7DT8:DA17DA18_BB A 7 ? B 18 ? A 8 ? B 17 ? 1 A DT 8 1_555 B DA 5 1_555 A DC 9 1_555 B DG 4 1_555 0.257 0.327 3.763 -6.897 -1.066 45.577 0.523 -1.005 3.680 -1.366 8.842 46.081 8 AA_DT8DC9:DG16DA17_BB A 8 ? B 17 ? A 9 ? B 16 ? 1 A DC 9 1_555 B DG 4 1_555 A DG 10 1_555 B DC 3 1_555 0.323 1.096 3.032 -2.454 4.572 23.922 1.231 -1.489 3.135 10.867 5.832 24.470 9 AA_DC9DG10:DC15DG16_BB A 9 ? B 16 ? A 10 ? B 15 ? 1 A DG 10 1_555 B DC 3 1_555 A DC 11 1_555 B DG 2 1_555 -2.132 0.101 3.426 -11.448 -10.396 39.223 1.365 1.623 3.738 -14.806 16.305 42.049 10 AA_DG10DC11:DG14DC15_BB A 10 ? B 15 ? A 11 ? B 14 ? 1 A DC 11 1_555 B DG 2 1_555 A DG 12 1_555 B DC 1 1_555 2.200 0.587 3.830 1.421 -7.828 35.979 2.169 -3.257 3.707 -12.485 -2.266 36.820 11 AA_DC11DG12:DC13DG14_BB A 11 ? B 14 ? A 12 ? B 13 ? # _atom_sites.entry_id 5BNA _atom_sites.fract_transf_matrix[1][1] 0.041391 _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] 0.025044 _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] 0.015124 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_sites_footnote.id _atom_sites_footnote.text 1 ;THE ANISOTROPIC TEMPERATURE FACTORS FOR THE PLATINUM ATOMS ARE AS FOLLOWS ATOM B11 B22 B33 B12 B13 B23 PT1 PTN 25 0.01510 0.00438 0.00138 0.00214 0.00056 0.00026 PT1 PTN 26 0.01545 0.00544 0.00131-0.00462-0.00072 0.00017 PT1 PTN 27 0.00729 0.00382 0.00120-0.00092-0.00060 0.00039 ; 2 'TEMPERATURE FACTORS WHICH WERE CALCULATED TO BE NON-POSITIVE-DEFINITE WERE ARBITRARILY SET TO 0.0 IN THE REFINEMENT PROCEDURE.' # loop_ _atom_type.symbol C N O P PT # loop_