data_7X9N # _model_server_result.job_id zTgOZTIWR7W0jlpBxTdOFA _model_server_result.datetime_utc '2024-11-24 00:52:32' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7x9n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 7X9N # _exptl.entry_id 7X9N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7X9N _cell.length_a 38.348 _cell.length_b 55.931 _cell.length_c 59.079 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7X9N _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 A O GLY 37 A GLY 37 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc2 A OE2 GLU 53 A GLU 53 1_555 F MG MG . A MG 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc3 A OE1 GLU 53 A GLU 53 1_555 G MG MG . A MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc4 A OE2 GLU 57 A GLU 57 1_555 E MG MG . A MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc5 A OE2 GLU 57 A GLU 57 1_555 G MG MG . A MG 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc6 C O2B 8DG . A 8DG 202 1_555 E MG MG . A MG 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.041 ? metalc ? metalc7 C O1A 8DG . A 8DG 202 1_555 E MG MG . A MG 204 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc8 C O1B 8DG . A 8DG 202 1_555 F MG MG . A MG 205 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc9 C O2B 8DG . A 8DG 202 1_555 G MG MG . A MG 206 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc10 D OP2 8OG . A 8OG 203 1_555 E MG MG . A MG 204 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc11 E MG MG . A MG 204 1_555 H O HOH . A HOH 314 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.16 ? metalc ? metalc12 E MG MG . A MG 204 1_555 H O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc13 E MG MG . A MG 204 1_555 H O HOH . A HOH 344 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc14 F MG MG . A MG 205 1_555 H O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc15 F MG MG . A MG 205 1_555 H O HOH . A HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc16 F MG MG . A MG 205 1_555 H O HOH . A HOH 400 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.276 ? metalc ? metalc17 F MG MG . A MG 205 1_555 H O HOH . A HOH 422 1_555 ? ? ? ? C ? ? ? ? ? ? ? 2.772 ? metalc ? metalc18 G MG MG . A MG 206 1_555 H O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.198 ? metalc ? metalc19 G MG MG . A MG 206 1_555 H O HOH . A HOH 314 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.983 ? metalc ? metalc20 G MG MG . A MG 206 1_555 H O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 8OG _chem_comp.mon_nstd_flag n _chem_comp.name "8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" _chem_comp.type 'dna linking' _chem_comp.pdbx_synonyms "8-OXO-7,8-DIHYDRO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag OP3 P 8OG sing 51 n n OP3 HOP3 8OG sing 52 n n P OP1 8OG doub 53 n n P OP2 8OG sing 54 n n P O5' 8OG sing 55 n n OP2 HOP2 8OG sing 56 n n O5' C5' 8OG sing 57 n n C5' C4' 8OG sing 58 n n C5' H5' 8OG sing 59 n n C5' "H5''" 8OG sing 60 n n C4' O4' 8OG sing 61 n n C4' C3' 8OG sing 62 n n C4' H4' 8OG sing 63 n n O4' C1' 8OG sing 64 n n C3' O3' 8OG sing 65 n n C3' C2' 8OG sing 66 n n C3' H3' 8OG sing 67 n n O3' HO3' 8OG sing 68 n n C2' C1' 8OG sing 69 n n C2' H2' 8OG sing 70 n n C2' "H2''" 8OG sing 71 n n C1' N9 8OG sing 72 n n C1' H1' 8OG sing 73 n n N9 C8 8OG sing 74 n n N9 C4 8OG sing 75 n n C8 N7 8OG sing 76 n n C8 O8 8OG doub 77 n n N7 C5 8OG sing 78 n n N7 H7 8OG sing 79 n n C5 C6 8OG sing 80 n n C5 C4 8OG doub 81 n n C6 O6 8OG doub 82 n n C6 N1 8OG sing 83 n n N1 C2 8OG sing 84 n n N1 H1 8OG sing 85 n n C2 N2 8OG sing 86 n n C2 N3 8OG doub 87 n n N2 H21 8OG sing 88 n n N2 H22 8OG sing 89 n n N3 C4 8OG sing 90 n n # _atom_sites.entry_id 7X9N _atom_sites.fract_transf_matrix[1][1] 0.026077 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017879 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.016926 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code B 2 SO4 A 1 201 1 SO4 SO4 . C 3 8DG A 1 202 25 8DG 8GT . D 4 8OG A 1 203 26 8OG 8OG . E 5 MG A 1 204 1 MG MG . F 5 MG A 1 205 2 MG MG . G 5 MG A 1 206 3 MG MG . H 6 HOH A 1 301 68 HOH HOH . H 6 HOH A 2 302 15 HOH HOH . H 6 HOH A 3 303 42 HOH HOH . H 6 HOH A 4 304 43 HOH HOH . H 6 HOH A 5 305 127 HOH HOH . H 6 HOH A 6 306 6 HOH HOH . H 6 HOH A 7 307 103 HOH HOH . H 6 HOH A 8 308 67 HOH HOH . H 6 HOH A 9 309 44 HOH HOH . H 6 HOH A 10 310 132 HOH HOH . H 6 HOH A 11 311 97 HOH HOH . H 6 HOH A 12 312 56 HOH HOH . H 6 HOH A 13 313 40 HOH HOH . H 6 HOH A 14 314 28 HOH HOH . H 6 HOH A 15 315 106 HOH HOH . H 6 HOH A 16 316 82 HOH HOH . H 6 HOH A 17 317 83 HOH HOH . H 6 HOH A 18 318 34 HOH HOH . H 6 HOH A 19 319 19 HOH HOH . H 6 HOH A 20 320 64 HOH HOH . H 6 HOH A 21 321 49 HOH HOH . H 6 HOH A 22 322 70 HOH HOH . H 6 HOH A 23 323 76 HOH HOH . H 6 HOH A 24 324 14 HOH HOH . H 6 HOH A 25 325 136 HOH HOH . H 6 HOH A 26 326 13 HOH HOH . H 6 HOH A 27 327 22 HOH HOH . H 6 HOH A 28 328 3 HOH HOH . H 6 HOH A 29 329 20 HOH HOH . H 6 HOH A 30 330 12 HOH HOH . H 6 HOH A 31 331 28 HOH HOH . H 6 HOH A 32 332 134 HOH HOH . H 6 HOH A 33 333 48 HOH HOH . H 6 HOH A 34 334 9 HOH HOH . H 6 HOH A 35 335 21 HOH HOH . H 6 HOH A 36 336 2 HOH HOH . H 6 HOH A 37 337 18 HOH HOH . H 6 HOH A 38 338 113 HOH HOH . H 6 HOH A 39 339 50 HOH HOH . H 6 HOH A 40 340 26 HOH HOH . H 6 HOH A 41 341 72 HOH HOH . H 6 HOH A 42 342 17 HOH HOH . H 6 HOH A 43 343 111 HOH HOH . H 6 HOH A 44 344 1 HOH HOH . H 6 HOH A 45 345 93 HOH HOH . H 6 HOH A 46 346 131 HOH HOH . H 6 HOH A 47 347 94 HOH HOH . H 6 HOH A 48 348 7 HOH HOH . H 6 HOH A 49 349 77 HOH HOH . H 6 HOH A 50 350 4 HOH HOH . H 6 HOH A 51 351 45 HOH HOH . H 6 HOH A 52 352 37 HOH HOH . H 6 HOH A 53 353 120 HOH HOH . H 6 HOH A 54 354 125 HOH HOH . H 6 HOH A 55 355 115 HOH HOH . H 6 HOH A 56 356 81 HOH HOH . H 6 HOH A 57 357 10 HOH HOH . H 6 HOH A 58 358 23 HOH HOH . H 6 HOH A 59 359 89 HOH HOH . H 6 HOH A 60 360 73 HOH HOH . H 6 HOH A 61 361 104 HOH HOH . H 6 HOH A 62 362 11 HOH HOH . H 6 HOH A 63 363 32 HOH HOH . H 6 HOH A 64 364 109 HOH HOH . H 6 HOH A 65 365 84 HOH HOH . H 6 HOH A 66 366 52 HOH HOH . H 6 HOH A 67 367 66 HOH HOH . H 6 HOH A 68 368 96 HOH HOH . H 6 HOH A 69 369 57 HOH HOH . H 6 HOH A 70 370 100 HOH HOH . H 6 HOH A 71 371 101 HOH HOH . H 6 HOH A 72 372 16 HOH HOH . H 6 HOH A 73 373 130 HOH HOH . H 6 HOH A 74 374 35 HOH HOH . H 6 HOH A 75 375 121 HOH HOH . H 6 HOH A 76 376 61 HOH HOH . H 6 HOH A 77 377 60 HOH HOH . H 6 HOH A 78 378 38 HOH HOH . H 6 HOH A 79 379 85 HOH HOH . H 6 HOH A 80 380 87 HOH HOH . H 6 HOH A 81 381 62 HOH HOH . H 6 HOH A 82 382 29 HOH HOH . H 6 HOH A 83 383 79 HOH HOH . H 6 HOH A 84 384 8 HOH HOH . H 6 HOH A 85 385 25 HOH HOH . H 6 HOH A 86 386 36 HOH HOH . H 6 HOH A 87 387 135 HOH HOH . H 6 HOH A 88 388 126 HOH HOH . H 6 HOH A 89 389 65 HOH HOH . H 6 HOH A 90 390 41 HOH HOH . H 6 HOH A 91 391 33 HOH HOH . H 6 HOH A 92 392 59 HOH HOH . H 6 HOH A 93 393 92 HOH HOH . H 6 HOH A 94 394 53 HOH HOH . H 6 HOH A 95 395 119 HOH HOH . H 6 HOH A 96 396 138 HOH HOH . H 6 HOH A 97 397 39 HOH HOH . H 6 HOH A 98 398 31 HOH HOH . H 6 HOH A 99 399 55 HOH HOH . H 6 HOH A 100 400 133 HOH HOH . H 6 HOH A 101 401 58 HOH HOH . H 6 HOH A 102 402 46 HOH HOH . H 6 HOH A 103 403 47 HOH HOH . H 6 HOH A 104 404 24 HOH HOH . H 6 HOH A 105 405 27 HOH HOH . H 6 HOH A 106 406 122 HOH HOH . H 6 HOH A 107 407 99 HOH HOH . H 6 HOH A 108 408 105 HOH HOH . H 6 HOH A 109 409 5 HOH HOH . H 6 HOH A 110 410 108 HOH HOH . H 6 HOH A 111 411 90 HOH HOH . H 6 HOH A 112 412 75 HOH HOH . H 6 HOH A 113 413 124 HOH HOH . H 6 HOH A 114 414 78 HOH HOH . H 6 HOH A 115 415 69 HOH HOH . H 6 HOH A 116 416 102 HOH HOH . H 6 HOH A 117 417 80 HOH HOH . H 6 HOH A 118 418 118 HOH HOH . H 6 HOH A 119 419 88 HOH HOH . H 6 HOH A 120 420 86 HOH HOH . H 6 HOH A 121 421 116 HOH HOH . H 6 HOH A 122 422 27 HOH HOH . H 6 HOH A 123 423 112 HOH HOH . H 6 HOH A 124 424 129 HOH HOH . H 6 HOH A 125 425 95 HOH HOH . H 6 HOH A 126 426 137 HOH HOH . H 6 HOH A 127 427 30 HOH HOH . H 6 HOH A 128 428 117 HOH HOH . H 6 HOH A 129 429 71 HOH HOH . H 6 HOH A 130 430 114 HOH HOH . H 6 HOH A 131 431 110 HOH HOH . H 6 HOH A 132 432 107 HOH HOH . H 6 HOH A 133 433 63 HOH HOH . H 6 HOH A 134 434 98 HOH HOH . H 6 HOH A 135 435 54 HOH HOH . H 6 HOH A 136 436 51 HOH HOH . H 6 HOH A 137 437 91 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O OP3 8OG . B . D 4 -9.916 2.021 24.15 0.3 13.49 ? OP3 8OG 203 A 1 HETATM 2 P P 8OG . B . D 4 -9.084 1.347 23.089 0.3 12.83 ? P 8OG 203 A 1 HETATM 3 O OP1 8OG . B . D 4 -9.848 0.945 21.851 0.3 15.96 ? OP1 8OG 203 A 1 HETATM 4 O OP2 8OG . B . D 4 -7.766 2.039 22.823 0.3 12.97 ? OP2 8OG 203 A 1 HETATM 5 O O5' 8OG . B . D 4 -8.67 -0.058 23.753 0.3 12.2 ? O5' 8OG 203 A 1 HETATM 6 C C5' 8OG . B . D 4 -7.461 -0.127 24.502 0.3 10.86 ? C5' 8OG 203 A 1 HETATM 7 C C4' 8OG . B . D 4 -7.62 -0.937 25.785 0.3 11.05 ? C4' 8OG 203 A 1 HETATM 8 O O4' 8OG . B . D 4 -6.314 -1.34 26.19 0.3 9.79 ? O4' 8OG 203 A 1 HETATM 9 C C3' 8OG . B . D 4 -8.2 -0.117 26.925 0.3 11.47 ? C3' 8OG 203 A 1 HETATM 10 O O3' 8OG . B . D 4 -9.053 -0.962 27.702 0.3 13.65 ? O3' 8OG 203 A 1 HETATM 11 C C2' 8OG . B . D 4 -7.014 0.265 27.787 0.3 9.54 ? C2' 8OG 203 A 1 HETATM 12 C C1' 8OG . B . D 4 -6.004 -0.835 27.487 0.3 10.29 ? C1' 8OG 203 A 1 HETATM 13 N N9 8OG . B . D 4 -4.636 -0.272 27.463 0.3 10.87 ? N9 8OG 203 A 1 HETATM 14 C C8 8OG . B . D 4 -3.663 -0.445 28.348 0.3 8.93 ? C8 8OG 203 A 1 HETATM 15 N N7 8OG . B . D 4 -2.515 0.183 28.044 0.3 9.46 ? N7 8OG 203 A 1 HETATM 16 C C5 8OG . B . D 4 -2.786 0.793 26.859 0.3 8.07 ? C5 8OG 203 A 1 HETATM 17 C C6 8OG . B . D 4 -2.035 1.594 26.005 0.3 8.56 ? C6 8OG 203 A 1 HETATM 18 O O6 8OG . B . D 4 -0.851 1.888 26.282 0.3 9.71 ? O6 8OG 203 A 1 HETATM 19 N N1 8OG . B . D 4 -2.582 2.056 24.872 0.3 7.72 ? N1 8OG 203 A 1 HETATM 20 C C2 8OG . B . D 4 -3.846 1.757 24.549 0.3 6.31 ? C2 8OG 203 A 1 HETATM 21 N N2 8OG . B . D 4 -4.381 2.227 23.399 0.3 9.1 ? N2 8OG 203 A 1 HETATM 22 N N3 8OG . B . D 4 -4.607 0.99 25.357 0.3 8.39 ? N3 8OG 203 A 1 HETATM 23 C C4 8OG . B . D 4 -4.099 0.489 26.504 0.3 9.07 ? C4 8OG 203 A 1 HETATM 24 O O8 8OG . B . D 4 -3.818 -1.139 29.422 0.3 9.85 ? O8 8OG 203 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 244 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 24 #