data_4ZF8
#
_model_server_result.job_id            nItAGIgcHC9B9PbBWFErCA 
_model_server_result.datetime_utc      '2024-11-12 21:03:35' 
_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          4zf8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":503}' 
#
_entry.id    4ZF8 
#
_exptl.entry_id    4ZF8 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              58.693 
_entity.id                          4 
_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            4ZF8 
_cell.length_a            55.899 
_cell.length_b            55.899 
_cell.length_c            711.033 
_cell.Z_PDB               12 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 4ZF8 
_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 
_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
? 4 D N N 
? 4 E N N 
? 4 F N N 
? 4 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 N THR 2 A THR 1 1_555 D NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? 
metalc ? metalc2 A OG1 THR 2 A THR 1 1_555 D NI NI . A NI 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? 
metalc ? metalc3 A NE2 HIS 139 A HIS 138 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? 
metalc ? metalc4 A OD1 ASP 215 A ASP 214 1_555 G NI NI . A NI 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? 
metalc ? metalc5 A NE2 HIS 237 A HIS 236 1_555 F NI NI . A NI 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? 
metalc ? metalc6 A NE2 HIS 286 A HIS 285 1_555 G NI NI . A NI 506 1_445 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? 
metalc ? metalc7 A OD2 ASP 339 A ASP 338 1_555 D NI NI . A NI 503 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.201 ? 
metalc ? metalc8 A OE1 GLU 349 A GLU 348 1_555 D NI NI . A NI 503 10_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.53 ? 
metalc ? metalc9 A SG CYS 401 A CYS 400 1_555 B FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? 
metalc ? metalc10 A NE2 HIS 427 A HIS 426 1_555 E NI NI . A NI 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc11 B FE HEM . A HEM 501 1_555 C N14 MYT . A MYT 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? 
#
_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                     4ZF8 
_atom_sites.fract_transf_matrix[1][1]    0.017889 
_atom_sites.fract_transf_matrix[1][2]    0.010328 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.020657 
_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]    0.001406 
_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 MYT A 1 502 501 MYT MYT . 
D 4 NI A 1 503 601 NI NI . 
E 4 NI A 1 504 602 NI NI . 
F 4 NI A 1 505 603 NI NI . 
G 4 NI A 1 506 604 NI NI . 
H 5 HOH A 1 601 752 HOH HOH . 
H 5 HOH A 2 602 720 HOH HOH . 
H 5 HOH A 3 603 751 HOH HOH . 
H 5 HOH A 4 604 703 HOH HOH . 
H 5 HOH A 5 605 704 HOH HOH . 
H 5 HOH A 6 606 754 HOH HOH . 
H 5 HOH A 7 607 713 HOH HOH . 
H 5 HOH A 8 608 719 HOH HOH . 
H 5 HOH A 9 609 717 HOH HOH . 
H 5 HOH A 10 610 749 HOH HOH . 
H 5 HOH A 11 611 743 HOH HOH . 
H 5 HOH A 12 612 782 HOH HOH . 
H 5 HOH A 13 613 733 HOH HOH . 
H 5 HOH A 14 614 768 HOH HOH . 
H 5 HOH A 15 615 783 HOH HOH . 
H 5 HOH A 16 616 770 HOH HOH . 
H 5 HOH A 17 617 739 HOH HOH . 
H 5 HOH A 18 618 737 HOH HOH . 
H 5 HOH A 19 619 707 HOH HOH . 
H 5 HOH A 20 620 750 HOH HOH . 
H 5 HOH A 21 621 718 HOH HOH . 
H 5 HOH A 22 622 774 HOH HOH . 
H 5 HOH A 23 623 773 HOH HOH . 
H 5 HOH A 24 624 729 HOH HOH . 
H 5 HOH A 25 625 744 HOH HOH . 
H 5 HOH A 26 626 725 HOH HOH . 
H 5 HOH A 27 627 710 HOH HOH . 
H 5 HOH A 28 628 766 HOH HOH . 
H 5 HOH A 29 629 723 HOH HOH . 
H 5 HOH A 30 630 721 HOH HOH . 
H 5 HOH A 31 631 727 HOH HOH . 
H 5 HOH A 32 632 702 HOH HOH . 
H 5 HOH A 33 633 759 HOH HOH . 
H 5 HOH A 34 634 778 HOH HOH . 
H 5 HOH A 35 635 715 HOH HOH . 
H 5 HOH A 36 636 716 HOH HOH . 
H 5 HOH A 37 637 709 HOH HOH . 
H 5 HOH A 38 638 732 HOH HOH . 
H 5 HOH A 39 639 711 HOH HOH . 
H 5 HOH A 40 640 706 HOH HOH . 
H 5 HOH A 41 641 728 HOH HOH . 
H 5 HOH A 42 642 734 HOH HOH . 
H 5 HOH A 43 643 701 HOH HOH . 
H 5 HOH A 44 644 731 HOH HOH . 
H 5 HOH A 45 645 775 HOH HOH . 
H 5 HOH A 46 646 730 HOH HOH . 
H 5 HOH A 47 647 714 HOH HOH . 
H 5 HOH A 48 648 740 HOH HOH . 
H 5 HOH A 49 649 726 HOH HOH . 
H 5 HOH A 50 650 772 HOH HOH . 
H 5 HOH A 51 651 756 HOH HOH . 
H 5 HOH A 52 652 735 HOH HOH . 
H 5 HOH A 53 653 742 HOH HOH . 
H 5 HOH A 54 654 771 HOH HOH . 
H 5 HOH A 55 655 757 HOH HOH . 
H 5 HOH A 56 656 765 HOH HOH . 
H 5 HOH A 57 657 722 HOH HOH . 
H 5 HOH A 58 658 712 HOH HOH . 
H 5 HOH A 59 659 762 HOH HOH . 
H 5 HOH A 60 660 760 HOH HOH . 
H 5 HOH A 61 661 745 HOH HOH . 
H 5 HOH A 62 662 755 HOH HOH . 
H 5 HOH A 63 663 748 HOH HOH . 
H 5 HOH A 64 664 779 HOH HOH . 
H 5 HOH A 65 665 705 HOH HOH . 
H 5 HOH A 66 666 741 HOH HOH . 
H 5 HOH A 67 667 708 HOH HOH . 
H 5 HOH A 68 668 746 HOH HOH . 
H 5 HOH A 69 669 780 HOH HOH . 
H 5 HOH A 70 670 724 HOH HOH . 
H 5 HOH A 71 671 758 HOH HOH . 
H 5 HOH A 72 672 747 HOH HOH . 
H 5 HOH A 73 673 763 HOH HOH . 
H 5 HOH A 74 674 776 HOH HOH . 
H 5 HOH A 75 675 738 HOH HOH . 
H 5 HOH A 76 676 777 HOH HOH . 
H 5 HOH A 77 677 764 HOH HOH . 
H 5 HOH A 78 678 769 HOH HOH . 
H 5 HOH A 79 679 761 HOH HOH . 
H 5 HOH A 80 680 753 HOH HOH . 
H 5 HOH A 81 681 736 HOH HOH . 
H 5 HOH A 82 682 767 HOH HOH . 
H 5 HOH A 83 683 781 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         D 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               12.903 
_atom_site.Cartn_y               -18.302 
_atom_site.Cartn_z               60.387 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        68.87 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_atom_site.auth_seq_id           503 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              8 
_model_server_stats.parse_time_ms           13 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           285 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           1 
#