data_1DNO # _entry.id 1DNO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.386 _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 1DNO pdb_00001dno 10.2210/pdb1dno/pdb NDB AH0007 ? ? RCSB RCSB010227 ? ? WWPDB D_1000010227 ? ? # 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 2000-04-10 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2024-02-07 # _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' 6 4 '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' 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_keywords 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.ptnr2_auth_asym_id' 7 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_auth_seq_id' 8 4 'Structure model' '_pdbx_struct_conn_angle.ptnr2_label_asym_id' 9 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_asym_id' 10 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_auth_seq_id' 11 4 'Structure model' '_pdbx_struct_conn_angle.ptnr3_label_asym_id' 12 4 'Structure model' '_pdbx_struct_conn_angle.value' 13 4 'Structure model' '_struct_conn.pdbx_dist_value' 14 4 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 15 4 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 16 4 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 17 4 'Structure model' '_struct_conn.ptnr1_label_asym_id' 18 4 'Structure model' '_struct_conn.ptnr1_label_atom_id' 19 4 'Structure model' '_struct_conn.ptnr1_label_comp_id' 20 4 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 21 4 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 22 4 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 23 4 'Structure model' '_struct_conn.ptnr2_label_asym_id' 24 4 'Structure model' '_struct_conn.ptnr2_label_atom_id' 25 4 'Structure model' '_struct_conn.ptnr2_label_comp_id' 26 4 'Structure model' '_struct_keywords.text' 27 4 'Structure model' '_struct_site.pdbx_auth_asym_id' 28 4 'Structure model' '_struct_site.pdbx_auth_comp_id' 29 4 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1DNO _pdbx_database_status.recvd_initial_deposition_date 1999-12-16 _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.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # _pdbx_database_related.db_name NDB _pdbx_database_related.db_id AHJ015 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Robinson, H.' 1 'Gao, Y.-G.' 2 'Sanishvili, R.' 3 'Joachimiak, A.' 4 'Wang, A.H.-J.' 5 # _citation.id primary _citation.title 'Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes.' _citation.journal_abbrev 'Nucleic Acids Res.' _citation.journal_volume 28 _citation.page_first 1760 _citation.page_last 1766 _citation.year 2000 _citation.journal_id_ASTM NARHAD _citation.country UK _citation.journal_id_ISSN 0305-1048 _citation.journal_id_CSD 0389 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 10734195 _citation.pdbx_database_id_DOI 10.1093/nar/28.8.1760 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Robinson, H.' 1 ? primary 'Gao, Y.G.' 2 ? primary 'Sanishvili, R.' 3 ? primary 'Joachimiak, A.' 4 ? primary 'Wang, A.H.' 5 ? # 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/RNA (5'-R(*GP*CP*GP)-D(*TP*AP*TP*AP*CP*GP*C)-3') ; 3093.005 2 ? ? ? ? 2 non-polymer syn 'MAGNESIUM ION' 24.305 4 ? ? ? ? 3 water nat water 18.015 120 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polydeoxyribonucleotide/polyribonucleotide hybrid' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code 'GCG(DT)(DA)(DT)(DA)(DC)(DG)(DC)' _entity_poly.pdbx_seq_one_letter_code_can GCGTATACGC _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 'MAGNESIUM ION' MG 3 water HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 G n 1 2 C n 1 3 G n 1 4 DT n 1 5 DA n 1 6 DT n 1 7 DA n 1 8 DC n 1 9 DG n 1 10 DC 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 C 'RNA linking' y "CYTIDINE-5'-MONOPHOSPHATE" ? 'C9 H14 N3 O8 P' 323.197 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 G 'RNA linking' y "GUANOSINE-5'-MONOPHOSPHATE" ? 'C10 H14 N5 O8 P' 363.221 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 G 1 1 1 G G A . n A 1 2 C 2 2 2 C C A . n A 1 3 G 3 3 3 G G A . n A 1 4 DT 4 4 4 DT T A . n A 1 5 DA 5 5 5 DA A A . n A 1 6 DT 6 6 6 DT T A . n A 1 7 DA 7 7 7 DA A A . n A 1 8 DC 8 8 8 DC C A . n A 1 9 DG 9 9 9 DG G A . n A 1 10 DC 10 10 10 DC C A . n B 1 1 G 1 11 11 G G B . n B 1 2 C 2 12 12 C C B . n B 1 3 G 3 13 13 G G B . n B 1 4 DT 4 14 14 DT T B . n B 1 5 DA 5 15 15 DA A B . n B 1 6 DT 6 16 16 DT T B . n B 1 7 DA 7 17 17 DA A B . n B 1 8 DC 8 18 18 DC C B . n B 1 9 DG 9 19 19 DG G B . n B 1 10 DC 10 20 20 DC C 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 MG 1 24 24 MG MO6 A . D 2 MG 1 21 21 MG MO6 B . E 2 MG 1 22 22 MG MO6 B . F 2 MG 1 23 23 MG MO6 B . G 3 HOH 1 102 102 HOH HOH A . G 3 HOH 2 104 104 HOH HOH A . G 3 HOH 3 105 105 HOH HOH A . G 3 HOH 4 107 107 HOH HOH A . G 3 HOH 5 111 111 HOH HOH A . G 3 HOH 6 113 113 HOH HOH A . G 3 HOH 7 114 114 HOH HOH A . G 3 HOH 8 117 117 HOH HOH A . G 3 HOH 9 120 120 HOH HOH A . G 3 HOH 10 121 121 HOH HOH A . G 3 HOH 11 122 122 HOH HOH A . G 3 HOH 12 123 123 HOH HOH A . G 3 HOH 13 125 125 HOH HOH A . G 3 HOH 14 126 126 HOH HOH A . G 3 HOH 15 127 127 HOH HOH A . G 3 HOH 16 128 128 HOH HOH A . G 3 HOH 17 130 130 HOH HOH A . G 3 HOH 18 131 131 HOH HOH A . G 3 HOH 19 136 136 HOH HOH A . G 3 HOH 20 137 137 HOH HOH A . G 3 HOH 21 139 139 HOH HOH A . G 3 HOH 22 141 141 HOH HOH A . G 3 HOH 23 145 145 HOH HOH A . G 3 HOH 24 150 150 HOH HOH A . G 3 HOH 25 154 154 HOH HOH A . G 3 HOH 26 156 156 HOH HOH A . G 3 HOH 27 158 158 HOH HOH A . G 3 HOH 28 161 161 HOH HOH A . G 3 HOH 29 164 164 HOH HOH A . G 3 HOH 30 172 172 HOH HOH A . G 3 HOH 31 173 173 HOH HOH A . G 3 HOH 32 177 177 HOH HOH A . G 3 HOH 33 178 178 HOH HOH A . G 3 HOH 34 179 179 HOH HOH A . G 3 HOH 35 183 183 HOH HOH A . G 3 HOH 36 184 184 HOH HOH A . G 3 HOH 37 188 188 HOH HOH A . G 3 HOH 38 189 189 HOH HOH A . G 3 HOH 39 190 190 HOH HOH A . G 3 HOH 40 192 192 HOH HOH A . G 3 HOH 41 193 193 HOH HOH A . G 3 HOH 42 205 22 HOH MO6 A . G 3 HOH 43 215 24 HOH MO6 A . G 3 HOH 44 216 24 HOH MO6 A . G 3 HOH 45 217 24 HOH MO6 A . G 3 HOH 46 218 24 HOH MO6 A . H 3 HOH 1 101 101 HOH HOH B . H 3 HOH 2 103 103 HOH HOH B . H 3 HOH 3 106 106 HOH HOH B . H 3 HOH 4 108 108 HOH HOH B . H 3 HOH 5 109 109 HOH HOH B . H 3 HOH 6 110 110 HOH HOH B . H 3 HOH 7 112 112 HOH HOH B . H 3 HOH 8 115 115 HOH HOH B . H 3 HOH 9 116 116 HOH HOH B . H 3 HOH 10 118 118 HOH HOH B . H 3 HOH 11 119 119 HOH HOH B . H 3 HOH 12 124 124 HOH HOH B . H 3 HOH 13 129 129 HOH HOH B . H 3 HOH 14 132 132 HOH HOH B . H 3 HOH 15 133 133 HOH HOH B . H 3 HOH 16 134 134 HOH HOH B . H 3 HOH 17 135 135 HOH HOH B . H 3 HOH 18 138 138 HOH HOH B . H 3 HOH 19 140 140 HOH HOH B . H 3 HOH 20 142 142 HOH HOH B . H 3 HOH 21 143 143 HOH HOH B . H 3 HOH 22 144 144 HOH HOH B . H 3 HOH 23 146 146 HOH HOH B . H 3 HOH 24 147 147 HOH HOH B . H 3 HOH 25 148 148 HOH HOH B . H 3 HOH 26 149 149 HOH HOH B . H 3 HOH 27 151 151 HOH HOH B . H 3 HOH 28 152 152 HOH HOH B . H 3 HOH 29 153 153 HOH HOH B . H 3 HOH 30 155 155 HOH HOH B . H 3 HOH 31 157 157 HOH HOH B . H 3 HOH 32 159 159 HOH HOH B . H 3 HOH 33 160 160 HOH HOH B . H 3 HOH 34 162 162 HOH HOH B . H 3 HOH 35 163 163 HOH HOH B . H 3 HOH 36 165 165 HOH HOH B . H 3 HOH 37 166 166 HOH HOH B . H 3 HOH 38 167 167 HOH HOH B . H 3 HOH 39 168 168 HOH HOH B . H 3 HOH 40 169 169 HOH HOH B . H 3 HOH 41 170 170 HOH HOH B . H 3 HOH 42 171 171 HOH HOH B . H 3 HOH 43 174 174 HOH HOH B . H 3 HOH 44 175 175 HOH HOH B . H 3 HOH 45 176 176 HOH HOH B . H 3 HOH 46 180 180 HOH HOH B . H 3 HOH 47 181 181 HOH HOH B . H 3 HOH 48 182 182 HOH HOH B . H 3 HOH 49 185 185 HOH HOH B . H 3 HOH 50 186 186 HOH HOH B . H 3 HOH 51 187 187 HOH HOH B . H 3 HOH 52 191 191 HOH HOH B . H 3 HOH 53 194 194 HOH HOH B . H 3 HOH 54 195 195 HOH HOH B . H 3 HOH 55 196 196 HOH HOH B . H 3 HOH 56 197 21 HOH MO6 B . H 3 HOH 57 198 21 HOH MO6 B . H 3 HOH 58 199 21 HOH MO6 B . H 3 HOH 59 200 21 HOH MO6 B . H 3 HOH 60 201 21 HOH MO6 B . H 3 HOH 61 202 21 HOH MO6 B . H 3 HOH 62 203 22 HOH MO6 B . H 3 HOH 63 204 22 HOH MO6 B . H 3 HOH 64 206 22 HOH MO6 B . H 3 HOH 65 207 22 HOH MO6 B . H 3 HOH 66 208 22 HOH MO6 B . H 3 HOH 67 209 23 HOH MO6 B . H 3 HOH 68 210 23 HOH MO6 B . H 3 HOH 69 211 23 HOH MO6 B . H 3 HOH 70 212 23 HOH MO6 B . H 3 HOH 71 213 23 HOH MO6 B . H 3 HOH 72 214 23 HOH MO6 B . H 3 HOH 73 219 24 HOH MO6 B . H 3 HOH 74 220 24 HOH MO6 B . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal d*TREK 'data scaling' . ? 1 HKL-2000 'data reduction' . ? 2 X-PLOR 'model building' . ? 3 SHELXL-97 refinement . ? 4 d*TREK 'data reduction' . ? 5 HKL-2000 'data scaling' . ? 6 X-PLOR phasing . ? 7 # _cell.entry_id 1DNO _cell.length_a 24.200 _cell.length_b 42.656 _cell.length_c 49.315 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1DNO _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1DNO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.87 _exptl_crystal.density_percent_sol 34.0 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.temp 298 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 6.5 _exptl_crystal_grow.pdbx_details '2-MPD, CACODYLATE, SPERMINE, MGCL2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K' _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 CACODYLATE ? ? ? 1 2 1 SPERMINE ? ? ? 1 3 1 MGCL2 ? ? ? 1 4 1 MPD ? ? ? 1 5 2 MPD ? ? ? # _diffrn.id 1 _diffrn.ambient_temp 110 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type CUSTOM-MADE _diffrn_detector.pdbx_collection_date 1999-11-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.03321 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID _diffrn_source.pdbx_wavelength 1.03321 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1DNO _reflns.observed_criterion_sigma_I 0.0 _reflns.observed_criterion_sigma_F 0.0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 1.40 _reflns.number_obs 10433 _reflns.number_all 10433 _reflns.percent_possible_obs 98.7 _reflns.pdbx_Rmerge_I_obs 0.067 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 37.3 _reflns.B_iso_Wilson_estimate 22.2 _reflns.pdbx_redundancy 11.7 _reflns.R_free_details ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # _reflns_shell.d_res_high 1.40 _reflns_shell.d_res_low 1.45 _reflns_shell.percent_possible_all 91.7 _reflns_shell.Rmerge_I_obs 0.092 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 23.8 _reflns_shell.pdbx_redundancy 11.0 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1DNO _refine.ls_number_reflns_obs 10433 _refine.ls_number_reflns_all 10433 _refine.pdbx_ls_sigma_I 0.0 _refine.pdbx_ls_sigma_F 0.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 20.0 _refine.ls_d_res_high 1.40 _refine.ls_percent_reflns_obs 98.7 _refine.ls_R_factor_obs 0.193 _refine.ls_R_factor_all 0.195 _refine.ls_R_factor_R_work 0.193 _refine.ls_R_factor_R_free 0.242 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5 _refine.ls_number_reflns_R_free 519 _refine.ls_number_parameters 2139 _refine.ls_number_restraints 1830 _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 'SHELXL SWAT OPTION' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method 'A POSTERIORI' _refine.details ? _refine.pdbx_starting_model 'NDB ID ADJ043' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'G.PARKINSON ET AL.' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _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.ls_redundancy_reflns_obs ? _refine.pdbx_overall_phase_error ? _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.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1DNO _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 0 _refine_analyze.occupancy_sum_non_hydrogen 534 _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _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 410 _refine_hist.pdbx_number_atoms_ligand 28 _refine_hist.number_atoms_solvent 96 _refine_hist.number_atoms_total 534 _refine_hist.d_res_high 1.40 _refine_hist.d_res_low 20.0 # 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 0.011 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.027 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.070 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.032 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1DNO _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff ? _pdbx_refine.R_factor_all_4sig_cutoff 0.193 _pdbx_refine.R_factor_obs_4sig_cutoff 0.191 _pdbx_refine.free_R_factor_4sig_cutoff 0.239 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 507 _pdbx_refine.number_reflns_obs_4sig_cutoff 10217 _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1DNO _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 1DNO _struct.title 'A-DNA/RNA DODECAMER R(GCG)D(TATACGC) MG BINDING SITES' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1DNO _struct_keywords.pdbx_keywords 'DNA-RNA HYBRID' _struct_keywords.text 'DNA CONFORMATION, RNA/DNA HYBRID, METAL IONS, DNA-RNA COMPLEX, DNA-RNA HYBRID COMPLEX, DNA-RNA HYBRID' # 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 2 ? G N N 3 ? H N N 3 ? # _struct_ref.id 1 _struct_ref.entity_id 1 _struct_ref.db_name PDB _struct_ref.db_code 1DNO _struct_ref.pdbx_db_accession 1DNO _struct_ref.pdbx_align_begin ? _struct_ref.pdbx_seq_one_letter_code ? _struct_ref.pdbx_db_isoform ? # 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 1DNO A 1 ? 10 ? 1DNO 1 ? 10 ? 1 10 2 1 1DNO B 1 ? 10 ? 1DNO 11 ? 20 ? 11 20 # _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 # _struct_biol.id 1 _struct_biol.details ? # 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 ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 24 A HOH 215 1_555 ? ? ? ? ? ? ? 2.045 ? ? metalc2 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 24 A HOH 216 1_555 ? ? ? ? ? ? ? 2.050 ? ? metalc3 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 24 A HOH 217 1_555 ? ? ? ? ? ? ? 2.051 ? ? metalc4 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 24 A HOH 218 1_555 ? ? ? ? ? ? ? 2.065 ? ? metalc5 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 24 B HOH 219 1_555 ? ? ? ? ? ? ? 2.060 ? ? metalc6 metalc ? ? C MG . MG ? ? ? 1_555 H HOH . O ? ? A MG 24 B HOH 220 1_555 ? ? ? ? ? ? ? 2.081 ? ? metalc7 metalc ? ? G HOH . O ? ? ? 1_555 E MG . MG ? ? A HOH 205 B MG 22 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc8 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 197 1_555 ? ? ? ? ? ? ? 2.067 ? ? metalc9 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 198 1_555 ? ? ? ? ? ? ? 2.060 ? ? metalc10 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 199 1_555 ? ? ? ? ? ? ? 2.072 ? ? metalc11 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 200 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc12 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 201 1_555 ? ? ? ? ? ? ? 2.061 ? ? metalc13 metalc ? ? D MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 21 B HOH 202 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc14 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 22 B HOH 203 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc15 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 22 B HOH 204 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc16 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 22 B HOH 206 1_555 ? ? ? ? ? ? ? 2.059 ? ? metalc17 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 22 B HOH 207 1_555 ? ? ? ? ? ? ? 2.067 ? ? metalc18 metalc ? ? E MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 22 B HOH 208 1_555 ? ? ? ? ? ? ? 2.053 ? ? metalc19 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 209 1_555 ? ? ? ? ? ? ? 2.066 ? ? metalc20 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 210 1_555 ? ? ? ? ? ? ? 2.057 ? ? metalc21 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 211 1_555 ? ? ? ? ? ? ? 2.072 ? ? metalc22 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 212 1_555 ? ? ? ? ? ? ? 2.058 ? ? metalc23 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 213 1_555 ? ? ? ? ? ? ? 2.048 ? ? metalc24 metalc ? ? F MG . MG ? ? ? 1_555 H HOH . O ? ? B MG 23 B HOH 214 1_555 ? ? ? ? ? ? ? 2.050 ? ? hydrog1 hydrog ? ? A G 1 N1 ? ? ? 1_555 B DC 10 N3 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog2 hydrog ? ? A G 1 N2 ? ? ? 1_555 B DC 10 O2 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog3 hydrog ? ? A G 1 O6 ? ? ? 1_555 B DC 10 N4 ? ? A G 1 B DC 20 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog4 hydrog ? ? A C 2 N3 ? ? ? 1_555 B DG 9 N1 ? ? A C 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog5 hydrog ? ? A C 2 N4 ? ? ? 1_555 B DG 9 O6 ? ? A C 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog6 hydrog ? ? A C 2 O2 ? ? ? 1_555 B DG 9 N2 ? ? A C 2 B DG 19 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog7 hydrog ? ? A G 3 N1 ? ? ? 1_555 B DC 8 N3 ? ? A G 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog8 hydrog ? ? A G 3 N2 ? ? ? 1_555 B DC 8 O2 ? ? A G 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog9 hydrog ? ? A G 3 O6 ? ? ? 1_555 B DC 8 N4 ? ? A G 3 B DC 18 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog10 hydrog ? ? A DT 4 N3 ? ? ? 1_555 B DA 7 N1 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog11 hydrog ? ? A DT 4 O4 ? ? ? 1_555 B DA 7 N6 ? ? A DT 4 B DA 17 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog12 hydrog ? ? A DA 5 N1 ? ? ? 1_555 B DT 6 N3 ? ? A DA 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog13 hydrog ? ? A DA 5 N6 ? ? ? 1_555 B DT 6 O4 ? ? A DA 5 B DT 16 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog14 hydrog ? ? A DT 6 N3 ? ? ? 1_555 B DA 5 N1 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog15 hydrog ? ? A DT 6 O4 ? ? ? 1_555 B DA 5 N6 ? ? A DT 6 B DA 15 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog16 hydrog ? ? A DA 7 N1 ? ? ? 1_555 B DT 4 N3 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog17 hydrog ? ? A DA 7 N6 ? ? ? 1_555 B DT 4 O4 ? ? A DA 7 B DT 14 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog18 hydrog ? ? A DC 8 N3 ? ? ? 1_555 B G 3 N1 ? ? A DC 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog19 hydrog ? ? A DC 8 N4 ? ? ? 1_555 B G 3 O6 ? ? A DC 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog20 hydrog ? ? A DC 8 O2 ? ? ? 1_555 B G 3 N2 ? ? A DC 8 B G 13 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog21 hydrog ? ? A DG 9 N1 ? ? ? 1_555 B C 2 N3 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog22 hydrog ? ? A DG 9 N2 ? ? ? 1_555 B C 2 O2 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog23 hydrog ? ? A DG 9 O6 ? ? ? 1_555 B C 2 N4 ? ? A DG 9 B C 12 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog24 hydrog ? ? A DC 10 N3 ? ? ? 1_555 B G 1 N1 ? ? A DC 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog25 hydrog ? ? A DC 10 N4 ? ? ? 1_555 B G 1 O6 ? ? A DC 10 B G 11 1_555 ? ? ? ? ? ? WATSON-CRICK ? ? ? hydrog26 hydrog ? ? A DC 10 O2 ? ? ? 1_555 B G 1 N2 ? ? A DC 10 B G 11 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 O ? G HOH . ? A HOH 215 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 216 ? 1_555 178.0 ? 2 O ? G HOH . ? A HOH 215 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 217 ? 1_555 89.7 ? 3 O ? G HOH . ? A HOH 216 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 217 ? 1_555 91.4 ? 4 O ? G HOH . ? A HOH 215 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 218 ? 1_555 88.8 ? 5 O ? G HOH . ? A HOH 216 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 218 ? 1_555 89.4 ? 6 O ? G HOH . ? A HOH 217 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? G HOH . ? A HOH 218 ? 1_555 90.7 ? 7 O ? G HOH . ? A HOH 215 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 219 ? 1_555 91.2 ? 8 O ? G HOH . ? A HOH 216 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 219 ? 1_555 87.8 ? 9 O ? G HOH . ? A HOH 217 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 219 ? 1_555 177.8 ? 10 O ? G HOH . ? A HOH 218 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 219 ? 1_555 91.3 ? 11 O ? G HOH . ? A HOH 215 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 93.0 ? 12 O ? G HOH . ? A HOH 216 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 88.8 ? 13 O ? G HOH . ? A HOH 217 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 86.8 ? 14 O ? G HOH . ? A HOH 218 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 176.8 ? 15 O ? H HOH . ? B HOH 219 ? 1_555 MG ? C MG . ? A MG 24 ? 1_555 O ? H HOH . ? B HOH 220 ? 1_555 91.2 ? 16 O ? G HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 203 ? 1_555 91.4 ? 17 O ? G HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 89.2 ? 18 O ? H HOH . ? B HOH 203 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 204 ? 1_555 176.8 ? 19 O ? G HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 90.0 ? 20 O ? H HOH . ? B HOH 203 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 88.1 ? 21 O ? H HOH . ? B HOH 204 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 206 ? 1_555 88.7 ? 22 O ? G HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 207 ? 1_555 176.6 ? 23 O ? H HOH . ? B HOH 203 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 207 ? 1_555 91.3 ? 24 O ? H HOH . ? B HOH 204 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 207 ? 1_555 88.2 ? 25 O ? H HOH . ? B HOH 206 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 207 ? 1_555 92.1 ? 26 O ? G HOH . ? A HOH 205 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 89.8 ? 27 O ? H HOH . ? B HOH 203 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 89.9 ? 28 O ? H HOH . ? B HOH 204 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 93.2 ? 29 O ? H HOH . ? B HOH 206 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 178.0 ? 30 O ? H HOH . ? B HOH 207 ? 1_555 MG ? E MG . ? B MG 22 ? 1_555 O ? H HOH . ? B HOH 208 ? 1_555 88.2 ? 31 O ? H HOH . ? B HOH 197 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 198 ? 1_555 178.7 ? 32 O ? H HOH . ? B HOH 197 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 199 ? 1_555 88.4 ? 33 O ? H HOH . ? B HOH 198 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 199 ? 1_555 92.6 ? 34 O ? H HOH . ? B HOH 197 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 200 ? 1_555 90.0 ? 35 O ? H HOH . ? B HOH 198 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 200 ? 1_555 89.2 ? 36 O ? H HOH . ? B HOH 199 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 200 ? 1_555 90.1 ? 37 O ? H HOH . ? B HOH 197 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 88.7 ? 38 O ? H HOH . ? B HOH 198 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 90.3 ? 39 O ? H HOH . ? B HOH 199 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 176.9 ? 40 O ? H HOH . ? B HOH 200 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 201 ? 1_555 90.9 ? 41 O ? H HOH . ? B HOH 197 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 89.3 ? 42 O ? H HOH . ? B HOH 198 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 91.4 ? 43 O ? H HOH . ? B HOH 199 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 88.4 ? 44 O ? H HOH . ? B HOH 200 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 178.4 ? 45 O ? H HOH . ? B HOH 201 ? 1_555 MG ? D MG . ? B MG 21 ? 1_555 O ? H HOH . ? B HOH 202 ? 1_555 90.6 ? 46 O ? H HOH . ? B HOH 209 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 210 ? 1_555 177.6 ? 47 O ? H HOH . ? B HOH 209 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 211 ? 1_555 88.8 ? 48 O ? H HOH . ? B HOH 210 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 211 ? 1_555 89.3 ? 49 O ? H HOH . ? B HOH 209 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 212 ? 1_555 88.3 ? 50 O ? H HOH . ? B HOH 210 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 212 ? 1_555 90.2 ? 51 O ? H HOH . ? B HOH 211 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 212 ? 1_555 89.5 ? 52 O ? H HOH . ? B HOH 209 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 213 ? 1_555 89.8 ? 53 O ? H HOH . ? B HOH 210 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 213 ? 1_555 92.0 ? 54 O ? H HOH . ? B HOH 211 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 213 ? 1_555 178.5 ? 55 O ? H HOH . ? B HOH 212 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 213 ? 1_555 89.8 ? 56 O ? H HOH . ? B HOH 209 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 214 ? 1_555 90.0 ? 57 O ? H HOH . ? B HOH 210 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 214 ? 1_555 91.4 ? 58 O ? H HOH . ? B HOH 211 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 214 ? 1_555 89.5 ? 59 O ? H HOH . ? B HOH 212 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 214 ? 1_555 178.1 ? 60 O ? H HOH . ? B HOH 213 ? 1_555 MG ? F MG . ? B MG 23 ? 1_555 O ? H HOH . ? B HOH 214 ? 1_555 91.1 ? # 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 MG 21 ? 6 'BINDING SITE FOR RESIDUE MG B 21' AC2 Software B MG 22 ? 6 'BINDING SITE FOR RESIDUE MG B 22' AC3 Software B MG 23 ? 6 'BINDING SITE FOR RESIDUE MG B 23' AC4 Software A MG 24 ? 6 'BINDING SITE FOR RESIDUE MG A 24' # 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 H . ? HOH B 197 . ? 1_555 ? 2 AC1 6 HOH H . ? HOH B 198 . ? 1_555 ? 3 AC1 6 HOH H . ? HOH B 199 . ? 1_555 ? 4 AC1 6 HOH H . ? HOH B 200 . ? 1_555 ? 5 AC1 6 HOH H . ? HOH B 201 . ? 1_555 ? 6 AC1 6 HOH H . ? HOH B 202 . ? 1_555 ? 7 AC2 6 HOH G . ? HOH A 205 . ? 1_555 ? 8 AC2 6 HOH H . ? HOH B 203 . ? 1_555 ? 9 AC2 6 HOH H . ? HOH B 204 . ? 1_555 ? 10 AC2 6 HOH H . ? HOH B 206 . ? 1_555 ? 11 AC2 6 HOH H . ? HOH B 207 . ? 1_555 ? 12 AC2 6 HOH H . ? HOH B 208 . ? 1_555 ? 13 AC3 6 HOH H . ? HOH B 209 . ? 1_555 ? 14 AC3 6 HOH H . ? HOH B 210 . ? 1_555 ? 15 AC3 6 HOH H . ? HOH B 211 . ? 1_555 ? 16 AC3 6 HOH H . ? HOH B 212 . ? 1_555 ? 17 AC3 6 HOH H . ? HOH B 213 . ? 1_555 ? 18 AC3 6 HOH H . ? HOH B 214 . ? 1_555 ? 19 AC4 6 HOH G . ? HOH A 215 . ? 1_555 ? 20 AC4 6 HOH G . ? HOH A 216 . ? 1_555 ? 21 AC4 6 HOH G . ? HOH A 217 . ? 1_555 ? 22 AC4 6 HOH G . ? HOH A 218 . ? 1_555 ? 23 AC4 6 HOH H . ? HOH B 219 . ? 1_555 ? 24 AC4 6 HOH H . ? HOH B 220 . ? 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 "C1'" A C 2 ? ? "O4'" A C 2 ? ? "C4'" A C 2 ? ? 105.24 109.70 -4.46 0.70 N 2 1 "O4'" A DT 4 ? ? "C4'" A DT 4 ? ? "C3'" A DT 4 ? ? 102.00 104.50 -2.50 0.40 N 3 1 C6 A DA 5 ? ? N1 A DA 5 ? ? C2 A DA 5 ? ? 122.43 118.60 3.83 0.60 N 4 1 C6 A DA 7 ? ? N1 A DA 7 ? ? C2 A DA 7 ? ? 122.25 118.60 3.65 0.60 N 5 1 C5 A DA 7 ? ? C6 A DA 7 ? ? N1 A DA 7 ? ? 114.64 117.70 -3.06 0.50 N 6 1 C5 A DA 7 ? ? C6 A DA 7 ? ? N6 A DA 7 ? ? 128.99 123.70 5.29 0.80 N 7 1 "O4'" A DC 8 ? ? "C4'" A DC 8 ? ? "C3'" A DC 8 ? ? 101.33 104.50 -3.17 0.40 N 8 1 "O4'" A DC 10 ? ? "C4'" A DC 10 ? ? "C3'" A DC 10 ? ? 100.64 104.50 -3.86 0.40 N 9 1 "O4'" A DC 10 ? ? "C1'" A DC 10 ? ? N1 A DC 10 ? ? 111.17 108.30 2.87 0.30 N 10 1 C6 A DC 10 ? ? N1 A DC 10 ? ? C2 A DC 10 ? ? 124.40 120.30 4.10 0.40 N 11 1 C5 A DC 10 ? ? C6 A DC 10 ? ? N1 A DC 10 ? ? 117.17 121.00 -3.83 0.50 N 12 1 C5 A DC 10 ? ? C4 A DC 10 ? ? N4 A DC 10 ? ? 115.18 120.20 -5.02 0.70 N 13 1 C6 B C 12 ? ? N1 B C 12 ? ? C2 B C 12 ? ? 117.10 120.30 -3.20 0.40 N 14 1 C5 B C 12 ? ? C6 B C 12 ? ? N1 B C 12 ? ? 126.06 121.00 5.06 0.50 N 15 1 "C5'" B G 13 ? ? "C4'" B G 13 ? ? "O4'" B G 13 ? ? 115.21 109.80 5.41 0.90 N 16 1 N1 B G 13 ? ? C6 B G 13 ? ? O6 B G 13 ? ? 116.19 119.90 -3.71 0.60 N 17 1 C5 B G 13 ? ? C6 B G 13 ? ? O6 B G 13 ? ? 132.52 128.60 3.92 0.60 N 18 1 "O4'" B DA 15 ? ? "C4'" B DA 15 ? ? "C3'" B DA 15 ? ? 102.09 104.50 -2.41 0.40 N 19 1 "O4'" B DT 16 ? ? "C4'" B DT 16 ? ? "C3'" B DT 16 ? ? 101.68 104.50 -2.82 0.40 N 20 1 "O4'" B DA 17 ? ? "C4'" B DA 17 ? ? "C3'" B DA 17 ? ? 101.83 104.50 -2.67 0.40 N 21 1 "O4'" B DC 18 ? ? "C4'" B DC 18 ? ? "C3'" B DC 18 ? ? 101.43 104.50 -3.07 0.40 N 22 1 "O4'" B DC 18 ? ? "C1'" B DC 18 ? ? N1 B DC 18 ? ? 110.19 108.30 1.89 0.30 N # loop_ _pdbx_validate_planes.id _pdbx_validate_planes.PDB_model_num _pdbx_validate_planes.auth_comp_id _pdbx_validate_planes.auth_asym_id _pdbx_validate_planes.auth_seq_id _pdbx_validate_planes.PDB_ins_code _pdbx_validate_planes.label_alt_id _pdbx_validate_planes.rmsd _pdbx_validate_planes.type 1 1 G A 3 ? ? 0.068 'SIDE CHAIN' 2 1 DA A 7 ? ? 0.063 'SIDE CHAIN' 3 1 G B 11 ? ? 0.073 'SIDE CHAIN' 4 1 DC B 20 ? ? 0.066 'SIDE CHAIN' # 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 C OP3 O N N 1 C P P N N 2 C OP1 O N N 3 C OP2 O N N 4 C "O5'" O N N 5 C "C5'" C N N 6 C "C4'" C N R 7 C "O4'" O N N 8 C "C3'" C N S 9 C "O3'" O N N 10 C "C2'" C N R 11 C "O2'" O N N 12 C "C1'" C N R 13 C N1 N N N 14 C C2 C N N 15 C O2 O N N 16 C N3 N N N 17 C C4 C N N 18 C N4 N N N 19 C C5 C N N 20 C C6 C N N 21 C HOP3 H N N 22 C HOP2 H N N 23 C "H5'" H N N 24 C "H5''" H N N 25 C "H4'" H N N 26 C "H3'" H N N 27 C "HO3'" H N N 28 C "H2'" H N N 29 C "HO2'" H N N 30 C "H1'" H N N 31 C H41 H N N 32 C H42 H N N 33 C H5 H N N 34 C H6 H N N 35 DA OP3 O N N 36 DA P P N N 37 DA OP1 O N N 38 DA OP2 O N N 39 DA "O5'" O N N 40 DA "C5'" C N N 41 DA "C4'" C N R 42 DA "O4'" O N N 43 DA "C3'" C N S 44 DA "O3'" O N N 45 DA "C2'" C N N 46 DA "C1'" C N R 47 DA N9 N Y N 48 DA C8 C Y N 49 DA N7 N Y N 50 DA C5 C Y N 51 DA C6 C Y N 52 DA N6 N N N 53 DA N1 N Y N 54 DA C2 C Y N 55 DA N3 N Y N 56 DA C4 C Y N 57 DA HOP3 H N N 58 DA HOP2 H N N 59 DA "H5'" H N N 60 DA "H5''" H N N 61 DA "H4'" H N N 62 DA "H3'" H N N 63 DA "HO3'" H N N 64 DA "H2'" H N N 65 DA "H2''" H N N 66 DA "H1'" H N N 67 DA H8 H N N 68 DA H61 H N N 69 DA H62 H N N 70 DA H2 H N N 71 DC OP3 O N N 72 DC P P N N 73 DC OP1 O N N 74 DC OP2 O N N 75 DC "O5'" O N N 76 DC "C5'" C N N 77 DC "C4'" C N R 78 DC "O4'" O N N 79 DC "C3'" C N S 80 DC "O3'" O N N 81 DC "C2'" C N N 82 DC "C1'" C N R 83 DC N1 N N N 84 DC C2 C N N 85 DC O2 O N N 86 DC N3 N N N 87 DC C4 C N N 88 DC N4 N N N 89 DC C5 C N N 90 DC C6 C N N 91 DC HOP3 H N N 92 DC HOP2 H N N 93 DC "H5'" H N N 94 DC "H5''" H N N 95 DC "H4'" H N N 96 DC "H3'" H N N 97 DC "HO3'" H N N 98 DC "H2'" H N N 99 DC "H2''" H N N 100 DC "H1'" H N N 101 DC H41 H N N 102 DC H42 H N N 103 DC H5 H N N 104 DC H6 H N N 105 DG OP3 O N N 106 DG P P N N 107 DG OP1 O N N 108 DG OP2 O N N 109 DG "O5'" O N N 110 DG "C5'" C N N 111 DG "C4'" C N R 112 DG "O4'" O N N 113 DG "C3'" C N S 114 DG "O3'" O N N 115 DG "C2'" C N N 116 DG "C1'" C N R 117 DG N9 N Y N 118 DG C8 C Y N 119 DG N7 N Y N 120 DG C5 C Y N 121 DG C6 C N N 122 DG O6 O N N 123 DG N1 N N N 124 DG C2 C N N 125 DG N2 N N N 126 DG N3 N N N 127 DG C4 C Y N 128 DG HOP3 H N N 129 DG HOP2 H N N 130 DG "H5'" H N N 131 DG "H5''" H N N 132 DG "H4'" H N N 133 DG "H3'" H N N 134 DG "HO3'" H N N 135 DG "H2'" H N N 136 DG "H2''" H N N 137 DG "H1'" H N N 138 DG H8 H N N 139 DG H1 H N N 140 DG H21 H N N 141 DG H22 H N N 142 DT OP3 O N N 143 DT P P N N 144 DT OP1 O N N 145 DT OP2 O N N 146 DT "O5'" O N N 147 DT "C5'" C N N 148 DT "C4'" C N R 149 DT "O4'" O N N 150 DT "C3'" C N S 151 DT "O3'" O N N 152 DT "C2'" C N N 153 DT "C1'" C N R 154 DT N1 N N N 155 DT C2 C N N 156 DT O2 O N N 157 DT N3 N N N 158 DT C4 C N N 159 DT O4 O N N 160 DT C5 C N N 161 DT C7 C N N 162 DT C6 C N N 163 DT HOP3 H N N 164 DT HOP2 H N N 165 DT "H5'" H N N 166 DT "H5''" H N N 167 DT "H4'" H N N 168 DT "H3'" H N N 169 DT "HO3'" H N N 170 DT "H2'" H N N 171 DT "H2''" H N N 172 DT "H1'" H N N 173 DT H3 H N N 174 DT H71 H N N 175 DT H72 H N N 176 DT H73 H N N 177 DT H6 H N N 178 G OP3 O N N 179 G P P N N 180 G OP1 O N N 181 G OP2 O N N 182 G "O5'" O N N 183 G "C5'" C N N 184 G "C4'" C N R 185 G "O4'" O N N 186 G "C3'" C N S 187 G "O3'" O N N 188 G "C2'" C N R 189 G "O2'" O N N 190 G "C1'" C N R 191 G N9 N Y N 192 G C8 C Y N 193 G N7 N Y N 194 G C5 C Y N 195 G C6 C N N 196 G O6 O N N 197 G N1 N N N 198 G C2 C N N 199 G N2 N N N 200 G N3 N N N 201 G C4 C Y N 202 G HOP3 H N N 203 G HOP2 H N N 204 G "H5'" H N N 205 G "H5''" H N N 206 G "H4'" H N N 207 G "H3'" H N N 208 G "HO3'" H N N 209 G "H2'" H N N 210 G "HO2'" H N N 211 G "H1'" H N N 212 G H8 H N N 213 G H1 H N N 214 G H21 H N N 215 G H22 H N N 216 HOH O O N N 217 HOH H1 H N N 218 HOH H2 H N N 219 MG MG MG N N 220 # 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 C OP3 P sing N N 1 C OP3 HOP3 sing N N 2 C P OP1 doub N N 3 C P OP2 sing N N 4 C P "O5'" sing N N 5 C OP2 HOP2 sing N N 6 C "O5'" "C5'" sing N N 7 C "C5'" "C4'" sing N N 8 C "C5'" "H5'" sing N N 9 C "C5'" "H5''" sing N N 10 C "C4'" "O4'" sing N N 11 C "C4'" "C3'" sing N N 12 C "C4'" "H4'" sing N N 13 C "O4'" "C1'" sing N N 14 C "C3'" "O3'" sing N N 15 C "C3'" "C2'" sing N N 16 C "C3'" "H3'" sing N N 17 C "O3'" "HO3'" sing N N 18 C "C2'" "O2'" sing N N 19 C "C2'" "C1'" sing N N 20 C "C2'" "H2'" sing N N 21 C "O2'" "HO2'" sing N N 22 C "C1'" N1 sing N N 23 C "C1'" "H1'" sing N N 24 C N1 C2 sing N N 25 C N1 C6 sing N N 26 C C2 O2 doub N N 27 C C2 N3 sing N N 28 C N3 C4 doub N N 29 C C4 N4 sing N N 30 C C4 C5 sing N N 31 C N4 H41 sing N N 32 C N4 H42 sing N N 33 C C5 C6 doub N N 34 C C5 H5 sing N N 35 C C6 H6 sing N N 36 DA OP3 P sing N N 37 DA OP3 HOP3 sing N N 38 DA P OP1 doub N N 39 DA P OP2 sing N N 40 DA P "O5'" sing N N 41 DA OP2 HOP2 sing N N 42 DA "O5'" "C5'" sing N N 43 DA "C5'" "C4'" sing N N 44 DA "C5'" "H5'" sing N N 45 DA "C5'" "H5''" sing N N 46 DA "C4'" "O4'" sing N N 47 DA "C4'" "C3'" sing N N 48 DA "C4'" "H4'" sing N N 49 DA "O4'" "C1'" sing N N 50 DA "C3'" "O3'" sing N N 51 DA "C3'" "C2'" sing N N 52 DA "C3'" "H3'" sing N N 53 DA "O3'" "HO3'" sing N N 54 DA "C2'" "C1'" sing N N 55 DA "C2'" "H2'" sing N N 56 DA "C2'" "H2''" sing N N 57 DA "C1'" N9 sing N N 58 DA "C1'" "H1'" sing N N 59 DA N9 C8 sing Y N 60 DA N9 C4 sing Y N 61 DA C8 N7 doub Y N 62 DA C8 H8 sing N N 63 DA N7 C5 sing Y N 64 DA C5 C6 sing Y N 65 DA C5 C4 doub Y N 66 DA C6 N6 sing N N 67 DA C6 N1 doub Y N 68 DA N6 H61 sing N N 69 DA N6 H62 sing N N 70 DA N1 C2 sing Y N 71 DA C2 N3 doub Y N 72 DA C2 H2 sing N N 73 DA N3 C4 sing Y N 74 DC OP3 P sing N N 75 DC OP3 HOP3 sing N N 76 DC P OP1 doub N N 77 DC P OP2 sing N N 78 DC P "O5'" sing N N 79 DC OP2 HOP2 sing N N 80 DC "O5'" "C5'" sing N N 81 DC "C5'" "C4'" sing N N 82 DC "C5'" "H5'" sing N N 83 DC "C5'" "H5''" sing N N 84 DC "C4'" "O4'" sing N N 85 DC "C4'" "C3'" sing N N 86 DC "C4'" "H4'" sing N N 87 DC "O4'" "C1'" sing N N 88 DC "C3'" "O3'" sing N N 89 DC "C3'" "C2'" sing N N 90 DC "C3'" "H3'" sing N N 91 DC "O3'" "HO3'" sing N N 92 DC "C2'" "C1'" sing N N 93 DC "C2'" "H2'" sing N N 94 DC "C2'" "H2''" sing N N 95 DC "C1'" N1 sing N N 96 DC "C1'" "H1'" sing N N 97 DC N1 C2 sing N N 98 DC N1 C6 sing N N 99 DC C2 O2 doub N N 100 DC C2 N3 sing N N 101 DC N3 C4 doub N N 102 DC C4 N4 sing N N 103 DC C4 C5 sing N N 104 DC N4 H41 sing N N 105 DC N4 H42 sing N N 106 DC C5 C6 doub N N 107 DC C5 H5 sing N N 108 DC C6 H6 sing N N 109 DG OP3 P sing N N 110 DG OP3 HOP3 sing N N 111 DG P OP1 doub N N 112 DG P OP2 sing N N 113 DG P "O5'" sing N N 114 DG OP2 HOP2 sing N N 115 DG "O5'" "C5'" sing N N 116 DG "C5'" "C4'" sing N N 117 DG "C5'" "H5'" sing N N 118 DG "C5'" "H5''" sing N N 119 DG "C4'" "O4'" sing N N 120 DG "C4'" "C3'" sing N N 121 DG "C4'" "H4'" sing N N 122 DG "O4'" "C1'" sing N N 123 DG "C3'" "O3'" sing N N 124 DG "C3'" "C2'" sing N N 125 DG "C3'" "H3'" sing N N 126 DG "O3'" "HO3'" sing N N 127 DG "C2'" "C1'" sing N N 128 DG "C2'" "H2'" sing N N 129 DG "C2'" "H2''" sing N N 130 DG "C1'" N9 sing N N 131 DG "C1'" "H1'" sing N N 132 DG N9 C8 sing Y N 133 DG N9 C4 sing Y N 134 DG C8 N7 doub Y N 135 DG C8 H8 sing N N 136 DG N7 C5 sing Y N 137 DG C5 C6 sing N N 138 DG C5 C4 doub Y N 139 DG C6 O6 doub N N 140 DG C6 N1 sing N N 141 DG N1 C2 sing N N 142 DG N1 H1 sing N N 143 DG C2 N2 sing N N 144 DG C2 N3 doub N N 145 DG N2 H21 sing N N 146 DG N2 H22 sing N N 147 DG N3 C4 sing N N 148 DT OP3 P sing N N 149 DT OP3 HOP3 sing N N 150 DT P OP1 doub N N 151 DT P OP2 sing N N 152 DT P "O5'" sing N N 153 DT OP2 HOP2 sing N N 154 DT "O5'" "C5'" sing N N 155 DT "C5'" "C4'" sing N N 156 DT "C5'" "H5'" sing N N 157 DT "C5'" "H5''" sing N N 158 DT "C4'" "O4'" sing N N 159 DT "C4'" "C3'" sing N N 160 DT "C4'" "H4'" sing N N 161 DT "O4'" "C1'" sing N N 162 DT "C3'" "O3'" sing N N 163 DT "C3'" "C2'" sing N N 164 DT "C3'" "H3'" sing N N 165 DT "O3'" "HO3'" sing N N 166 DT "C2'" "C1'" sing N N 167 DT "C2'" "H2'" sing N N 168 DT "C2'" "H2''" sing N N 169 DT "C1'" N1 sing N N 170 DT "C1'" "H1'" sing N N 171 DT N1 C2 sing N N 172 DT N1 C6 sing N N 173 DT C2 O2 doub N N 174 DT C2 N3 sing N N 175 DT N3 C4 sing N N 176 DT N3 H3 sing N N 177 DT C4 O4 doub N N 178 DT C4 C5 sing N N 179 DT C5 C7 sing N N 180 DT C5 C6 doub N N 181 DT C7 H71 sing N N 182 DT C7 H72 sing N N 183 DT C7 H73 sing N N 184 DT C6 H6 sing N N 185 G OP3 P sing N N 186 G OP3 HOP3 sing N N 187 G P OP1 doub N N 188 G P OP2 sing N N 189 G P "O5'" sing N N 190 G OP2 HOP2 sing N N 191 G "O5'" "C5'" sing N N 192 G "C5'" "C4'" sing N N 193 G "C5'" "H5'" sing N N 194 G "C5'" "H5''" sing N N 195 G "C4'" "O4'" sing N N 196 G "C4'" "C3'" sing N N 197 G "C4'" "H4'" sing N N 198 G "O4'" "C1'" sing N N 199 G "C3'" "O3'" sing N N 200 G "C3'" "C2'" sing N N 201 G "C3'" "H3'" sing N N 202 G "O3'" "HO3'" sing N N 203 G "C2'" "O2'" sing N N 204 G "C2'" "C1'" sing N N 205 G "C2'" "H2'" sing N N 206 G "O2'" "HO2'" sing N N 207 G "C1'" N9 sing N N 208 G "C1'" "H1'" sing N N 209 G N9 C8 sing Y N 210 G N9 C4 sing Y N 211 G C8 N7 doub Y N 212 G C8 H8 sing N N 213 G N7 C5 sing Y N 214 G C5 C6 sing N N 215 G C5 C4 doub Y N 216 G C6 O6 doub N N 217 G C6 N1 sing N N 218 G N1 C2 sing N N 219 G N1 H1 sing N N 220 G C2 N2 sing N N 221 G C2 N3 doub N N 222 G N2 H21 sing N N 223 G N2 H22 sing N N 224 G N3 C4 sing N N 225 HOH O H1 sing N N 226 HOH O H2 sing N N 227 # _ndb_struct_conf_na.entry_id 1DNO _ndb_struct_conf_na.feature 'a-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 G 1 1_555 B DC 10 1_555 -0.092 -0.112 0.113 3.180 -6.173 -3.804 1 A_G1:DC20_B A 1 ? B 20 ? 19 1 1 A C 2 1_555 B DG 9 1_555 0.205 -0.138 -0.019 4.319 -13.011 1.118 2 A_C2:DG19_B A 2 ? B 19 ? 19 1 1 A G 3 1_555 B DC 8 1_555 -0.217 -0.090 -0.054 -11.408 -15.384 0.375 3 A_G3:DC18_B A 3 ? B 18 ? 19 1 1 A DT 4 1_555 B DA 7 1_555 -0.129 -0.092 0.170 -4.502 -9.488 -0.917 4 A_DT4:DA17_B A 4 ? B 17 ? 20 1 1 A DA 5 1_555 B DT 6 1_555 -0.020 -0.109 0.186 1.052 -15.087 3.360 5 A_DA5:DT16_B A 5 ? B 16 ? 20 1 1 A DT 6 1_555 B DA 5 1_555 0.032 0.005 0.270 8.772 -14.410 12.181 6 A_DT6:DA15_B A 6 ? B 15 ? 20 1 1 A DA 7 1_555 B DT 4 1_555 -0.039 -0.085 0.118 10.106 -12.218 5.009 7 A_DA7:DT14_B A 7 ? B 14 ? 20 1 1 A DC 8 1_555 B G 3 1_555 0.164 -0.162 -0.132 10.667 -18.872 0.426 8 A_DC8:G13_B A 8 ? B 13 ? 19 1 1 A DG 9 1_555 B C 2 1_555 -0.135 -0.225 0.156 -2.757 -13.106 0.504 9 A_DG9:C12_B A 9 ? B 12 ? 19 1 1 A DC 10 1_555 B G 1 1_555 0.270 -0.090 0.220 -2.976 -0.345 -2.813 10 A_DC10:G11_B A 10 ? B 11 ? 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 G 1 1_555 B DC 10 1_555 A C 2 1_555 B DG 9 1_555 0.542 -1.718 3.205 1.218 2.123 38.305 -2.870 -0.677 3.124 3.231 -1.854 38.380 1 AA_G1C2:DG19DC20_BB A 1 ? B 20 ? A 2 ? B 19 ? 1 A C 2 1_555 B DG 9 1_555 A G 3 1_555 B DC 8 1_555 -0.594 -1.913 3.421 -1.902 16.303 28.110 -6.005 0.762 2.065 30.499 3.558 32.468 2 AA_C2G3:DC18DG19_BB A 2 ? B 19 ? A 3 ? B 18 ? 1 A G 3 1_555 B DC 8 1_555 A DT 4 1_555 B DA 7 1_555 -0.502 -1.156 3.125 -3.139 4.731 31.593 -2.889 0.380 2.960 8.603 5.707 32.086 3 AA_G3DT4:DA17DC18_BB A 3 ? B 18 ? A 4 ? B 17 ? 1 A DT 4 1_555 B DA 7 1_555 A DA 5 1_555 B DT 6 1_555 0.450 -1.212 3.007 1.250 13.861 29.502 -4.205 -0.619 2.244 25.507 -2.300 32.554 4 AA_DT4DA5:DT16DA17_BB A 4 ? B 17 ? A 5 ? B 16 ? 1 A DA 5 1_555 B DT 6 1_555 A DT 6 1_555 B DA 5 1_555 0.897 -1.214 3.092 0.126 8.264 32.666 -3.310 -1.531 2.716 14.407 -0.219 33.668 5 AA_DA5DT6:DA15DT16_BB A 5 ? B 16 ? A 6 ? B 15 ? 1 A DT 6 1_555 B DA 5 1_555 A DA 7 1_555 B DT 4 1_555 -0.775 -1.114 3.062 -0.056 16.087 29.537 -4.192 1.335 2.183 29.002 0.102 33.548 6 AA_DT6DA7:DT14DA15_BB A 6 ? B 15 ? A 7 ? B 14 ? 1 A DA 7 1_555 B DT 4 1_555 A DC 8 1_555 B G 3 1_555 -0.351 -1.206 3.283 2.066 5.024 31.700 -3.053 0.993 3.033 9.113 -3.748 32.150 7 AA_DA7DC8:G13DT14_BB A 7 ? B 14 ? A 8 ? B 13 ? 1 A DC 8 1_555 B G 3 1_555 A DG 9 1_555 B C 2 1_555 -0.124 -1.526 3.475 -3.774 13.535 31.798 -4.586 -0.356 2.626 23.332 6.505 34.691 8 AA_DC8DG9:C12G13_BB A 8 ? B 13 ? A 9 ? B 12 ? 1 A DG 9 1_555 B C 2 1_555 A DC 10 1_555 B G 1 1_555 0.453 -1.894 3.357 2.779 -0.409 35.914 -3.003 -0.325 3.402 -0.662 -4.498 36.020 9 AA_DG9DC10:G11C12_BB A 9 ? B 12 ? A 10 ? B 11 ? # _atom_sites.entry_id 1DNO _atom_sites.fract_transf_matrix[1][1] 0.041322 _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] 0.023443 _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] 0.020278 _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_type.symbol C MG N O P # loop_