data_473D
#
_model_server_result.job_id            SQFf34h-dWg-yVHUsekA0w 
_model_server_result.datetime_utc      '2024-10-18 13:24:42' 
_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          473d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"F","auth_seq_id":351}' 
#
_entry.id    473D 
#
_exptl.entry_id    473D 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              58.693 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NICKEL (II) ION' 
_entity.pdbx_number_of_molecules    4 
_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            473D 
_cell.length_a            25.18 
_cell.length_b            39.11 
_cell.length_c            53.47 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 473D 
_symmetry.cell_setting             orthorhombic 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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,I 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 D N N 
? 2 F N N 
? 2 G N 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 N7 DG 2 A DG 2 1_555 D NI NI . A NI 352 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? 
metalc ? metalc2 A OP2 DT 5 A DT 5 4_465 G NI NI . B NI 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? 
metalc ? metalc3 A N7 DG 10 A DG 10 1_555 C NI NI . A NI 350 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc4 C NI NI . A NI 350 1_555 H O HOH . A HOH 1000 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? 
metalc ? metalc5 C NI NI . A NI 350 1_555 H O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? 
metalc ? metalc6 C NI NI . A NI 350 1_555 H O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc7 C NI NI . A NI 350 1_555 H O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? 
metalc ? metalc8 C NI NI . A NI 350 1_555 H O HOH . A HOH 1004 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? 
metalc ? metalc9 D NI NI . A NI 352 1_555 H O HOH . A HOH 1010 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc10 D NI NI . A NI 352 1_555 H O HOH . A HOH 1011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? 
metalc ? metalc11 D NI NI . A NI 352 1_555 H O HOH . A HOH 1012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? 
metalc ? metalc12 D NI NI . A NI 352 1_555 H O HOH . A HOH 1013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? 
metalc ? metalc13 D NI NI . A NI 352 1_555 H O HOH . A HOH 1014 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.933 ? 
metalc ? metalc14 B N7 DG 2 B DG 12 1_555 F NI NI . B NI 351 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? 
metalc ? metalc15 B N7 DG 10 B DG 20 1_555 G NI NI . B NI 353 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? 
metalc ? metalc16 F NI NI . B NI 351 1_555 I O HOH . B HOH 1005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc17 F NI NI . B NI 351 1_555 I O HOH . B HOH 1006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? 
metalc ? metalc18 F NI NI . B NI 351 1_555 I O HOH . B HOH 1007 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? 
metalc ? metalc19 F NI NI . B NI 351 1_555 I O HOH . B HOH 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.008 ? 
metalc ? metalc20 F NI NI . B NI 351 1_555 I O HOH . B HOH 1009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? 
metalc ? metalc21 G NI NI . B NI 353 1_555 I O HOH . B HOH 1015 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? 
metalc ? metalc22 G NI NI . B NI 353 1_555 I O HOH . B HOH 1016 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.055 ? 
metalc ? metalc23 G NI NI . B NI 353 1_555 I O HOH . B HOH 1017 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? 
metalc ? metalc24 G NI NI . B NI 353 1_555 I O HOH . B HOH 1018 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? 
hydrog WATSON-CRICK hydrog1 A N1 DG 2 A DG 2 1_555 B N3 DC 9 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 DG 2 A DG 2 1_555 B O2 DC 9 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 DG 2 A DG 2 1_555 B N4 DC 9 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N3 DT 3 A DT 3 1_555 B N1 DA 8 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A O4 DT 3 A DT 3 1_555 B N6 DA 8 B DA 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A N1 DA 4 A DA 4 1_555 B N3 DT 7 B DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N6 DA 4 A DA 4 1_555 B O4 DT 7 B DT 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N3 DT 5 A DT 5 1_555 B N1 DA 6 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O4 DT 5 A DT 5 1_555 B N6 DA 6 B DA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DA 6 A DA 6 1_555 B N3 DT 5 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N6 DA 6 A DA 6 1_555 B O4 DT 5 B DT 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N3 DT 7 A DT 7 1_555 B N1 DA 4 B DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A O4 DT 7 A DT 7 1_555 B N6 DA 4 B DA 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N1 DA 8 A DA 8 1_555 B N3 DT 3 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N6 DA 8 A DA 8 1_555 B O4 DT 3 B DT 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N3 DC 9 A DC 9 1_555 B N1 DG 2 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N4 DC 9 A DC 9 1_555 B O6 DG 2 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O2 DC 9 A DC 9 1_555 B N2 DG 2 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_chem_comp.formula           'Ni 2' 
_chem_comp.formula_weight    58.693 
_chem_comp.id                NI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NICKEL (II) ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     473D 
_atom_sites.fract_transf_matrix[1][1]    0.039714 
_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]    0.025569 
_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]    0.018702 
_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
C 2 NI A 1 350 350 NI NI . 
D 2 NI A 1 352 352 NI NI . 
E 3 NT B 1 21 21 NT NT . 
F 2 NI B 1 351 351 NI NI . 
G 2 NI B 1 353 353 NI NI . 
H 4 HOH A 1 1000 1000 HOH HOH . 
H 4 HOH A 2 1001 1001 HOH HOH . 
H 4 HOH A 3 1002 1002 HOH HOH . 
H 4 HOH A 4 1003 1003 HOH HOH . 
H 4 HOH A 5 1004 1004 HOH HOH . 
H 4 HOH A 6 1010 1010 HOH HOH . 
H 4 HOH A 7 1011 1011 HOH HOH . 
H 4 HOH A 8 1012 1012 HOH HOH . 
H 4 HOH A 9 1013 1013 HOH HOH . 
H 4 HOH A 10 1014 1014 HOH HOH . 
H 4 HOH A 11 1022 1022 HOH HOH . 
H 4 HOH A 12 1023 1023 HOH HOH . 
H 4 HOH A 13 1024 1024 HOH HOH . 
H 4 HOH A 14 1025 1025 HOH HOH . 
H 4 HOH A 15 1026 1026 HOH HOH . 
H 4 HOH A 16 1029 1029 HOH HOH . 
H 4 HOH A 17 1030 1030 HOH HOH . 
H 4 HOH A 18 1031 1031 HOH HOH . 
H 4 HOH A 19 1032 1032 HOH HOH . 
H 4 HOH A 20 1033 1033 HOH HOH . 
H 4 HOH A 21 1034 1034 HOH HOH . 
H 4 HOH A 22 1035 1035 HOH HOH . 
H 4 HOH A 23 1037 1037 HOH HOH . 
H 4 HOH A 24 1038 1038 HOH HOH . 
H 4 HOH A 25 1041 1041 HOH HOH . 
H 4 HOH A 26 1043 1043 HOH HOH . 
H 4 HOH A 27 1050 1050 HOH HOH . 
H 4 HOH A 28 1051 1051 HOH HOH . 
H 4 HOH A 29 1052 1052 HOH HOH . 
H 4 HOH A 30 1054 1054 HOH HOH . 
H 4 HOH A 31 1055 1055 HOH HOH . 
H 4 HOH A 32 1060 1060 HOH HOH . 
H 4 HOH A 33 1061 1061 HOH HOH . 
H 4 HOH A 34 1063 1063 HOH HOH . 
H 4 HOH A 35 1064 1064 HOH HOH . 
H 4 HOH A 36 1065 1065 HOH HOH . 
H 4 HOH A 37 1069 1069 HOH HOH . 
H 4 HOH A 38 1070 1070 HOH HOH . 
H 4 HOH A 39 1075 1075 HOH HOH . 
H 4 HOH A 40 1077 1077 HOH HOH . 
H 4 HOH A 41 1078 1078 HOH HOH . 
I 4 HOH B 1 1005 1005 HOH HOH . 
I 4 HOH B 2 1006 1006 HOH HOH . 
I 4 HOH B 3 1007 1007 HOH HOH . 
I 4 HOH B 4 1008 1008 HOH HOH . 
I 4 HOH B 5 1009 1009 HOH HOH . 
I 4 HOH B 6 1015 1015 HOH HOH . 
I 4 HOH B 7 1016 1016 HOH HOH . 
I 4 HOH B 8 1017 1017 HOH HOH . 
I 4 HOH B 9 1018 1018 HOH HOH . 
I 4 HOH B 10 1019 1019 HOH HOH . 
I 4 HOH B 11 1020 1020 HOH HOH . 
I 4 HOH B 12 1021 1021 HOH HOH . 
I 4 HOH B 13 1027 1027 HOH HOH . 
I 4 HOH B 14 1028 1028 HOH HOH . 
I 4 HOH B 15 1036 1036 HOH HOH . 
I 4 HOH B 16 1039 1039 HOH HOH . 
I 4 HOH B 17 1040 1040 HOH HOH . 
I 4 HOH B 18 1042 1042 HOH HOH . 
I 4 HOH B 19 1044 1044 HOH HOH . 
I 4 HOH B 20 1045 1045 HOH HOH . 
I 4 HOH B 21 1046 1046 HOH HOH . 
I 4 HOH B 22 1047 1047 HOH HOH . 
I 4 HOH B 23 1048 1048 HOH HOH . 
I 4 HOH B 24 1049 1049 HOH HOH . 
I 4 HOH B 25 1053 1053 HOH HOH . 
I 4 HOH B 26 1056 1056 HOH HOH . 
I 4 HOH B 27 1057 1057 HOH HOH . 
I 4 HOH B 28 1058 1058 HOH HOH . 
I 4 HOH B 29 1059 1059 HOH HOH . 
I 4 HOH B 30 1062 1062 HOH HOH . 
I 4 HOH B 31 1066 1066 HOH HOH . 
I 4 HOH B 32 1067 1067 HOH HOH . 
I 4 HOH B 33 1068 1068 HOH HOH . 
I 4 HOH B 34 1071 1071 HOH HOH . 
I 4 HOH B 35 1072 1072 HOH HOH . 
I 4 HOH B 36 1073 1073 HOH HOH . 
I 4 HOH B 37 1074 1074 HOH HOH . 
I 4 HOH B 38 1076 1076 HOH HOH . 
I 4 HOH B 39 1079 1079 HOH HOH . 
I 4 HOH B 40 1080 1080 HOH HOH . 
I 4 HOH B 41 1081 1081 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           NI 
_atom_site.label_atom_id         NI 
_atom_site.label_comp_id         NI 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         F 
_atom_site.label_entity_id       2 
_atom_site.Cartn_x               7.403 
_atom_site.Cartn_y               25.527 
_atom_site.Cartn_z               20.892 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        18.6 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           351 
_atom_site.auth_asym_id          B 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              85 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    9 
_model_server_stats.query_time_ms           334 
_model_server_stats.encode_time_ms          11 
_model_server_stats.element_count           1 
#