data_XCC # _chem_comp.id XCC _chem_comp.name "FE(4)-NI(1)-S(4) CLUSTER" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "Fe4 Ni S4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "C CLUSTER" _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date 2002-12-20 _chem_comp.pdbx_modified_date 2026-09-01 _chem_comp.pdbx_ambiguous_flag Y _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 410.333 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XCC _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details MetalCoord _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1MJG _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _chem_comp.pdbx_pcm Y _chem_comp.pdbx_comp_type "metal-containing ligand" # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_ordinal XCC FE1 FE1 FE ? 0 N N N N N N -13.814 67.139 32.487 -13.850 67.136 32.429 FE1 XCC 1 XCC FE2 FE2 FE ? 0 N N N N N N -12.141 69.628 30.894 -11.862 69.776 31.351 FE2 XCC 2 XCC FE3 FE3 FE ? 0 N N N N N N -16.396 68.111 32.601 -16.272 68.117 32.509 FE3 XCC 3 XCC FE4 FE4 FE ? 0 N N N N N N -15.199 67.464 30.091 -15.210 67.449 30.217 FE4 XCC 4 XCC S1 S1 S -2 1 N N N N N N -16.392 69.333 30.632 -16.429 69.344 30.583 S1 XCC 5 XCC S2 S2 S -2 1 N N N N N N -15.687 66.042 31.863 -15.750 65.997 31.880 S2 XCC 6 XCC S4 S4 S -2 1 N N N N N N -14.620 68.896 33.751 -14.498 68.895 33.730 S4 XCC 7 XCC S3 S3 S -2 1 N N N N N N -12.995 67.946 30.449 -12.996 67.935 30.482 S3 XCC 8 XCC NI NI NI ? 0 N N N N N N -14.603 70.103 31.807 -14.863 70.103 31.929 NI XCC 9 # 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 _chem_comp_bond.pdbx_metal_coordination_flag _chem_comp_bond.pdbx_metal_pi_flag XCC FE1 S2 SING N N 1 Y N XCC FE1 S4 SING N N 2 Y N XCC FE1 S3 SING N N 3 Y N XCC FE2 S3 SING N N 4 Y N XCC FE3 S1 SING N N 5 Y N XCC FE3 S2 SING N N 6 Y N XCC FE3 S4 SING N N 7 Y N XCC FE4 S1 SING N N 8 Y N XCC FE4 S2 SING N N 9 Y N XCC FE4 S3 SING N N 10 Y N XCC S1 NI SING N N 11 Y N XCC S4 NI SING N N 12 Y N # loop_ _pdbx_chem_comp_descriptor.comp_id _pdbx_chem_comp_descriptor.type _pdbx_chem_comp_descriptor.program _pdbx_chem_comp_descriptor.program_version _pdbx_chem_comp_descriptor.descriptor XCC InChI InChI 1.06 InChI=1S/4Fe.Ni.4S XCC InChIKey InChI 1.06 QGLWBXDZIHZONR-UHFFFAOYSA-N XCC SMILES_CANONICAL CACTVS 3.385 "[Fe]S[Fe].S1[Fe]S[Ni]S[Fe]1" XCC SMILES CACTVS 3.385 "[Fe]S[Fe].S1[Fe]S[Ni]S[Fe]1" XCC SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "[S]1([Fe]2[S]3[Fe]1[S]4[Fe]3[S]2[Ni]4)[Fe]" XCC SMILES "OpenEye OEToolkits" 3.1.0.0 "[S]1([Fe]2[S]3[Fe]1[S]4[Fe]3[S]2[Ni]4)[Fe]" # _pdbx_chem_comp_identifier.comp_id XCC _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "1$l^{3},3$l^{3},5$l^{3},7$l^{3}-tetrathia-4$l^{2}-nickela-2$l^{3},6$l^{3},8$l^{3}-triferratetracyclo[4.2.0.0^{2,5}.0^{3,8}]octan-7-yliron" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XCC _pdbx_chem_comp_synonyms.name "C CLUSTER" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_atom_coordination.geometry_id _pdbx_chem_comp_atom_coordination.comp_id _pdbx_chem_comp_atom_coordination.atom_id _pdbx_chem_comp_atom_coordination.number _pdbx_chem_comp_atom_coordination.geometry_calculated _pdbx_chem_comp_atom_coordination.geometry_generic _pdbx_chem_comp_atom_coordination.geometry_abbr _pdbx_chem_comp_atom_coordination.provenance _pdbx_chem_comp_atom_coordination.representative_entry_id 1 XCC FE1 4 tetrahedron tetrahedral TET FindGeo 9IYL 1 XCC FE1 4 tetrahedral tetrahedral TET MetalCoord 9IYL 2 XCC FE2 4 tetrahedron tetrahedral TET FindGeo 1OAO 2 XCC FE2 4 tetrahedral tetrahedral TET MetalCoord 1OAO 3 XCC FE2 4 trigonal-pyramid "trigonal pyramidal" TPY MetalCoord 6ONC 3 XCC FE2 4 "trigonal bipyramid with a vacancy (axial)" "trigonal pyramidal" BVA FindGeo 3I01 4 XCC FE3 4 tetrahedral tetrahedral TET MetalCoord 9IYR 4 XCC FE3 4 tetrahedron tetrahedral TET FindGeo 6ONC 5 XCC FE4 4 tetrahedron tetrahedral TET FindGeo 9IYL 5 XCC FE4 4 tetrahedral tetrahedral TET MetalCoord 6ONC 6 XCC FE4 5 trigonal-bipyramid "trigonal bipyramidal" TBP MetalCoord 9IYL 7 XCC NI 4 "square plane" "square planar" SPL FindGeo 3I04 8 XCC NI 4 tetrahedral tetrahedral TET MetalCoord 1OAO 9 XCC NI 4 trigonal-pyramid "trigonal pyramidal" TPY MetalCoord 6VWY # loop_ _pdbx_chem_comp_atom_coordination_sphere.id _pdbx_chem_comp_atom_coordination_sphere.geometry_id _pdbx_chem_comp_atom_coordination_sphere.comp_id _pdbx_chem_comp_atom_coordination_sphere.atom_id _pdbx_chem_comp_atom_coordination_sphere.descriptor _pdbx_chem_comp_atom_coordination_sphere.provenance _pdbx_chem_comp_atom_coordination_sphere.representative_entry_id 1 1 XCC FE1 "@TET{Fe,S,S,S,S}" MetalCoord 9IYL 2 2 XCC FE2 "@TET{Fe,S,S,S,S}" MetalCoord 1OAO 3 3 XCC FE2 "@TPY{Fe,O,S,S,N}" MetalCoord 6ONC 4 3 XCC FE2 "@TPY{Fe,N,S,S,S}" MetalCoord 6VWY 5 4 XCC FE3 "@TET{Fe,S,S,S,S}" MetalCoord 9IYR 6 5 XCC FE4 "@TET{Fe,S,S,S,S}" MetalCoord 6ONC 7 6 XCC FE4 "@TBP{Fe,S,S,S,S,S}" MetalCoord 9IYL 8 8 XCC NI "@TET{Ni,C,S,S,S}" MetalCoord 1OAO 9 8 XCC NI "@TET{Ni,S,S,S,S}" MetalCoord 1MJG 10 8 XCC NI "@TET{Ni,O,S,S,S}" MetalCoord 6X5K 11 9 XCC NI "@TPY{Ni,S,S,S,S}" MetalCoord 6VWY # loop_ _pdbx_chem_comp_pcm.pcm_id _pdbx_chem_comp_pcm.comp_id _pdbx_chem_comp_pcm.modified_residue_id _pdbx_chem_comp_pcm.type _pdbx_chem_comp_pcm.category _pdbx_chem_comp_pcm.polypeptide_position _pdbx_chem_comp_pcm.comp_id_linking_atom _pdbx_chem_comp_pcm.modified_residue_id_linking_atom _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession _pdbx_chem_comp_pcm.position 1 XCC CYS None "Metal coordination" "Any position" FE1 SG ? ? "Amino-acid side chain" 2 XCC CYS None "Metal coordination" "Any position" FE2 SG ? ? "Amino-acid side chain" 3 XCC CYS None "Metal coordination" "Any position" FE3 SG ? ? "Amino-acid side chain" 4 XCC CYS None "Metal coordination" "Any position" FE4 SG ? ? "Amino-acid side chain" 5 XCC CYS None "Metal coordination" "Any position" NI SG ? ? "Amino-acid side chain" 6 XCC HIS None "Metal coordination" "Any position" FE1 NE2 ? ? "Amino-acid side chain" 7 XCC HIS None "Metal coordination" "Any position" FE2 NE2 ? ? "Amino-acid side chain" 8 XCC SER None "Metal coordination" "Any position" FE3 OG ? ? "Amino-acid side chain" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site XCC "Modify synonyms" 2020-06-11 PDBE XCC "Modify descriptor" 2023-09-23 RCSB XCC "Other modification" 2026-05-11 RCSB XCC "Other modification" 2026-07-17 RCSB XCC "Other modification" 2026-07-31 RCSB XCC "Other modification" 2026-09-01 RCSB #