data_4ZFA # _model_server_result.job_id JKLIXObGgiSK3Uvf-yLIRw _model_server_result.datetime_utc '2024-11-26 17:17:25' _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 4zfa # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 4ZFA # _exptl.entry_id 4ZFA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 5 _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 120 _cell.entry_id 4ZFA _cell.length_a 55.503 _cell.length_b 55.503 _cell.length_c 717.749 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4ZFA _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_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 ? 5 E N N ? 5 F N N ? 5 G N N ? 5 H 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 N THR 2 A THR 1 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc2 A OG1 THR 2 A THR 1 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.156 ? metalc ? metalc3 A NE2 HIS 139 A HIS 138 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc4 A NE2 HIS 237 A HIS 236 1_555 H NI NI . A NI 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc5 A OD2 ASP 339 A ASP 338 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc6 A OE2 GLU 349 A GLU 348 1_555 E NI NI . A NI 504 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc7 A SG CYS 401 A CYS 400 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc8 A NE2 HIS 427 A HIS 426 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? metalc ? metalc9 B FE HEM . A HEM 501 1_555 D O2 EDO . A EDO 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.797 ? metalc ? metalc10 G NI NI . A NI 506 1_555 I O HOH . A HOH 650 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? # _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 4ZFA _atom_sites.fract_transf_matrix[1][1] 0.018017 _atom_sites.fract_transf_matrix[1][2] 0.010402 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020804 _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] 0.001393 _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 HEM A 1 501 500 HEM HEM . C 3 1PE A 1 502 501 1PE 1PE . D 4 EDO A 1 503 502 EDO EDO . E 5 NI A 1 504 601 NI NI . F 5 NI A 1 505 602 NI NI . G 5 NI A 1 506 603 NI NI . H 5 NI A 1 507 604 NI NI . I 6 HOH A 1 601 740 HOH HOH . I 6 HOH A 2 602 726 HOH HOH . I 6 HOH A 3 603 705 HOH HOH . I 6 HOH A 4 604 706 HOH HOH . I 6 HOH A 5 605 731 HOH HOH . I 6 HOH A 6 606 712 HOH HOH . I 6 HOH A 7 607 743 HOH HOH . I 6 HOH A 8 608 728 HOH HOH . I 6 HOH A 9 609 732 HOH HOH . I 6 HOH A 10 610 733 HOH HOH . I 6 HOH A 11 611 714 HOH HOH . I 6 HOH A 12 612 709 HOH HOH . I 6 HOH A 13 613 727 HOH HOH . I 6 HOH A 14 614 739 HOH HOH . I 6 HOH A 15 615 718 HOH HOH . I 6 HOH A 16 616 721 HOH HOH . I 6 HOH A 17 617 744 HOH HOH . I 6 HOH A 18 618 746 HOH HOH . I 6 HOH A 19 619 730 HOH HOH . I 6 HOH A 20 620 702 HOH HOH . I 6 HOH A 21 621 738 HOH HOH . I 6 HOH A 22 622 748 HOH HOH . I 6 HOH A 23 623 711 HOH HOH . I 6 HOH A 24 624 749 HOH HOH . I 6 HOH A 25 625 720 HOH HOH . I 6 HOH A 26 626 704 HOH HOH . I 6 HOH A 27 627 719 HOH HOH . I 6 HOH A 28 628 701 HOH HOH . I 6 HOH A 29 629 757 HOH HOH . I 6 HOH A 30 630 715 HOH HOH . I 6 HOH A 31 631 703 HOH HOH . I 6 HOH A 32 632 717 HOH HOH . I 6 HOH A 33 633 729 HOH HOH . I 6 HOH A 34 634 707 HOH HOH . I 6 HOH A 35 635 710 HOH HOH . I 6 HOH A 36 636 736 HOH HOH . I 6 HOH A 37 637 747 HOH HOH . I 6 HOH A 38 638 751 HOH HOH . I 6 HOH A 39 639 723 HOH HOH . I 6 HOH A 40 640 750 HOH HOH . I 6 HOH A 41 641 742 HOH HOH . I 6 HOH A 42 642 741 HOH HOH . I 6 HOH A 43 643 745 HOH HOH . I 6 HOH A 44 644 725 HOH HOH . I 6 HOH A 45 645 737 HOH HOH . I 6 HOH A 46 646 752 HOH HOH . I 6 HOH A 47 647 724 HOH HOH . I 6 HOH A 48 648 754 HOH HOH . I 6 HOH A 49 649 722 HOH HOH . I 6 HOH A 50 650 735 HOH HOH . I 6 HOH A 51 651 713 HOH HOH . I 6 HOH A 52 652 755 HOH HOH . I 6 HOH A 53 653 734 HOH HOH . I 6 HOH A 54 654 716 HOH HOH . I 6 HOH A 55 655 708 HOH HOH . I 6 HOH A 56 656 753 HOH HOH . I 6 HOH A 57 657 756 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 H _atom_site.label_entity_id 5 _atom_site.Cartn_x -23.577 _atom_site.Cartn_y 20.944 _atom_site.Cartn_z 22.266 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 79.72 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 507 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 60 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 285 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #