3GM6
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in complex with phosphate
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0005509 | molecular_function | calcium ion binding |
| A | 0016491 | molecular_function | oxidoreductase activity |
| A | 0019331 | biological_process | anaerobic respiration, using ammonium as electron donor |
| A | 0019645 | biological_process | anaerobic electron transport chain |
| A | 0020037 | molecular_function | heme binding |
| A | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
| A | 0042128 | biological_process | nitrate assimilation |
| A | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
| A | 0042597 | cellular_component | periplasmic space |
| A | 0046872 | molecular_function | metal ion binding |
| B | 0005509 | molecular_function | calcium ion binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0019331 | biological_process | anaerobic respiration, using ammonium as electron donor |
| B | 0019645 | biological_process | anaerobic electron transport chain |
| B | 0020037 | molecular_function | heme binding |
| B | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
| B | 0042128 | biological_process | nitrate assimilation |
| B | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
| B | 0042597 | cellular_component | periplasmic space |
| B | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC A 1004 |
| Chain | Residue |
| A | HIS113 |
| A | ARG242 |
| A | CYS299 |
| A | HIS300 |
| A | TYR303 |
| A | HIS361 |
| A | ASN486 |
| A | PO4526 |
| A | HOH545 |
| A | HOH713 |
| A | HOH714 |
| A | ALA114 |
| A | HOH720 |
| A | HEC1006 |
| A | ASP125 |
| A | HIS126 |
| A | VAL129 |
| A | ARG131 |
| A | CYS184 |
| A | CYS187 |
| A | LYS188 |
| site_id | AC2 |
| Number of Residues | 14 |
| Details | BINDING SITE FOR RESIDUE HEC A 1005 |
| Chain | Residue |
| A | HIS70 |
| A | GLN73 |
| A | LEU225 |
| A | CYS227 |
| A | CYS230 |
| A | HIS231 |
| A | MET384 |
| A | LYS386 |
| A | TYR395 |
| A | THR396 |
| A | HIS398 |
| A | HOH818 |
| A | HOH846 |
| A | HEC1003 |
| site_id | AC3 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE HEC A 1006 |
| Chain | Residue |
| A | SER84 |
| A | PRO116 |
| A | ARG117 |
| A | HIS119 |
| A | PHE121 |
| A | MET122 |
| A | ASP125 |
| A | CYS187 |
| A | LYS188 |
| A | LEU225 |
| A | MET229 |
| A | CYS296 |
| A | CYS299 |
| A | HIS300 |
| A | HIS383 |
| A | MET384 |
| A | GLN400 |
| A | HOH534 |
| A | HOH551 |
| A | HOH553 |
| A | HOH708 |
| A | HEC1004 |
| A | HEC1007 |
| site_id | AC4 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC A 1007 |
| Chain | Residue |
| A | PHE367 |
| A | HIS372 |
| A | ALA378 |
| A | CYS379 |
| A | CYS382 |
| A | HIS383 |
| A | THR402 |
| A | ARG404 |
| A | LYS431 |
| A | ASN486 |
| A | PHE490 |
| A | HIS491 |
| A | HOH551 |
| A | HOH708 |
| A | HOH709 |
| A | HOH710 |
| A | HOH717 |
| A | HOH721 |
| A | HEC1006 |
| site_id | AC5 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE HEC A 1008 |
| Chain | Residue |
| A | ASN141 |
| A | TRP142 |
| A | GLN143 |
| A | VAL371 |
| A | HIS372 |
| A | PRO403 |
| A | ALA410 |
| A | CYS411 |
| A | CYS414 |
| A | HIS415 |
| A | TRP418 |
| A | ILE427 |
| A | HOH652 |
| site_id | AC6 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC A 1002 |
| Chain | Residue |
| A | LEU194 |
| A | PHE228 |
| A | PRO233 |
| A | HIS234 |
| A | ARG239 |
| A | PHE274 |
| A | ARG276 |
| A | ARG282 |
| A | HOH643 |
| A | HOH680 |
| A | HOH984 |
| A | HEC1001 |
| A | HEC1003 |
| A | CYS14 |
| A | PHE15 |
| A | HIS18 |
| A | HIS25 |
| A | VAL33 |
| A | ASN34 |
| A | CYS35 |
| A | CYS38 |
| A | HIS39 |
| site_id | AC7 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE HEC A 1003 |
| Chain | Residue |
| A | LYS29 |
| A | HIS30 |
| A | HIS37 |
| A | ALA65 |
| A | CYS66 |
| A | THR68 |
| A | CYS69 |
| A | HIS70 |
| A | HIS231 |
| A | ALA236 |
| A | HOH905 |
| A | HEC1002 |
| A | HEC1005 |
| A | HOH1030 |
| A | HOH1040 |
| site_id | AC8 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC A 1001 |
| Chain | Residue |
| A | GLN13 |
| A | CYS14 |
| A | CYS17 |
| A | HIS18 |
| A | HIS39 |
| A | HIS44 |
| A | ALA48 |
| A | SER49 |
| A | SER50 |
| A | ARG52 |
| A | ARG56 |
| A | PRO57 |
| A | THR59 |
| A | LEU194 |
| A | ARG276 |
| A | GLY277 |
| A | HOH646 |
| A | HOH685 |
| A | HOH973 |
| A | HOH982 |
| A | HEC1002 |
| site_id | AC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PO4 A 526 |
| Chain | Residue |
| A | PHE109 |
| A | ARG131 |
| A | TYR303 |
| A | GLN360 |
| A | HIS361 |
| A | HOH715 |
| A | HOH720 |
| A | HOH732 |
| A | HEC1004 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 527 |
| Chain | Residue |
| A | GLU302 |
| A | TYR303 |
| A | LYS358 |
| A | GLN360 |
| A | HOH821 |
| A | HOH822 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MPD A 528 |
| Chain | Residue |
| A | ARG87 |
| A | GLN138 |
| A | PHE139 |
| A | TRP142 |
| A | ARG497 |
| A | HOH910 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MPD A 529 |
| Chain | Residue |
| A | LYS431 |
| A | ASN432 |
| A | HIS435 |
| site_id | BC4 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC B 1004 |
| Chain | Residue |
| B | HIS113 |
| B | ALA114 |
| B | ASP125 |
| B | HIS126 |
| B | VAL129 |
| B | ARG131 |
| B | CYS184 |
| B | CYS187 |
| B | LYS188 |
| B | ARG242 |
| B | CYS299 |
| B | HIS300 |
| B | TYR303 |
| B | HIS361 |
| B | ASN486 |
| B | PO4526 |
| B | HOH620 |
| B | HOH766 |
| B | HOH767 |
| B | HOH773 |
| B | HEC1006 |
| site_id | BC5 |
| Number of Residues | 15 |
| Details | BINDING SITE FOR RESIDUE HEC B 1005 |
| Chain | Residue |
| B | HIS70 |
| B | GLN73 |
| B | LEU225 |
| B | CYS227 |
| B | CYS230 |
| B | HIS231 |
| B | MET384 |
| B | TYR395 |
| B | THR396 |
| B | HIS398 |
| B | HOH583 |
| B | HOH871 |
| B | HOH899 |
| B | HEC1003 |
| B | HOH1053 |
| site_id | BC6 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE HEC B 1006 |
| Chain | Residue |
| B | SER84 |
| B | PRO116 |
| B | ARG117 |
| B | HIS119 |
| B | PHE121 |
| B | MET122 |
| B | ASP125 |
| B | CYS187 |
| B | MET229 |
| B | CYS296 |
| B | CYS299 |
| B | HIS300 |
| B | HIS383 |
| B | MET384 |
| B | HOH609 |
| B | HOH627 |
| B | HOH629 |
| B | HOH761 |
| B | HEC1004 |
| B | HEC1007 |
| site_id | BC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC B 1007 |
| Chain | Residue |
| B | PHE367 |
| B | HIS372 |
| B | ALA378 |
| B | CYS379 |
| B | CYS382 |
| B | HIS383 |
| B | THR402 |
| B | ARG404 |
| B | LYS431 |
| B | ASN486 |
| B | PHE490 |
| B | HIS491 |
| B | HOH627 |
| B | HOH761 |
| B | HOH762 |
| B | HOH763 |
| B | HOH770 |
| B | HOH774 |
| B | HEC1006 |
| site_id | BC8 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE HEC B 1008 |
| Chain | Residue |
| B | ASN141 |
| B | TRP142 |
| B | GLN143 |
| B | VAL371 |
| B | HIS372 |
| B | PRO403 |
| B | ALA410 |
| B | CYS411 |
| B | CYS414 |
| B | HIS415 |
| B | TRP418 |
| B | ILE427 |
| B | HOH555 |
| site_id | BC9 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC B 1002 |
| Chain | Residue |
| B | CYS14 |
| B | PHE15 |
| B | HIS18 |
| B | ILE21 |
| B | HIS25 |
| B | VAL33 |
| B | ASN34 |
| B | CYS35 |
| B | CYS38 |
| B | HIS39 |
| B | LEU194 |
| B | PHE228 |
| B | PRO233 |
| B | HIS234 |
| B | ARG239 |
| B | PHE274 |
| B | ARG276 |
| B | ARG282 |
| B | HOH699 |
| B | HOH733 |
| B | HEC1001 |
| B | HEC1003 |
| site_id | CC1 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE HEC B 1003 |
| Chain | Residue |
| A | THR68 |
| B | LYS29 |
| B | HIS30 |
| B | HIS37 |
| B | ALA65 |
| B | CYS66 |
| B | CYS69 |
| B | HIS70 |
| B | CYS227 |
| B | HIS231 |
| B | ALA236 |
| B | HOH534 |
| B | HOH573 |
| B | HOH598 |
| B | HOH959 |
| B | HEC1002 |
| B | HEC1005 |
| B | HOH1059 |
| site_id | CC2 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE HEC B 1001 |
| Chain | Residue |
| B | GLN13 |
| B | CYS14 |
| B | CYS17 |
| B | HIS18 |
| B | HIS39 |
| B | HIS44 |
| B | VAL45 |
| B | ALA48 |
| B | SER49 |
| B | ARG51 |
| B | ARG51 |
| B | ARG52 |
| B | MET53 |
| B | ARG56 |
| B | PRO57 |
| B | THR59 |
| B | LEU194 |
| B | GLN275 |
| B | ARG276 |
| B | HOH702 |
| B | HOH733 |
| B | HOH738 |
| B | HOH916 |
| B | HOH917 |
| B | HEC1002 |
| B | HOH1037 |
| B | HOH1046 |
| site_id | CC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PO4 B 526 |
| Chain | Residue |
| B | PHE109 |
| B | ARG131 |
| B | TYR303 |
| B | GLN360 |
| B | HIS361 |
| B | HOH768 |
| B | HOH773 |
| B | HOH785 |
| B | HEC1004 |
| site_id | CC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 527 |
| Chain | Residue |
| B | GLU302 |
| B | TYR303 |
| B | LYS358 |
| B | GLN360 |
| B | HOH874 |
| B | HOH875 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MPD B 528 |
| Chain | Residue |
| B | ARG87 |
| B | GLN138 |
| B | PHE139 |
| B | TRP142 |
| B | ARG497 |
| B | HOH964 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MRD B 529 |
| Chain | Residue |
| B | SER95 |
| B | LYS431 |
| B | HIS435 |
| B | HOH556 |
| B | HOH1065 |
Functional Information from SwissProt/UniProt
| site_id | SWS_FT_FI1 |
| Number of Residues | 32 |
| Details | Binding site: {"description":"covalent","evidences":[{"source":"PubMed","id":"19393666","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20944237","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22281743","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4L38","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3Y","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI2 |
| Number of Residues | 28 |
| Details | Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"19393666","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20944237","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22281743","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4L38","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3Y","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI3 |
| Number of Residues | 2 |
| Details | Binding site: {"description":"axial binding residue","evidences":[{"source":"PubMed","id":"19393666","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20944237","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22281743","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI4 |
| Number of Residues | 8 |
| Details | Binding site: {"evidences":[{"source":"PubMed","id":"19393666","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20944237","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22281743","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4L38","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4L3Y","evidenceCode":"ECO:0007744"}]} |
| Chain | Residue | Details |
| site_id | SWS_FT_FI5 |
| Number of Residues | 4 |
| Details | Cross-link: {"description":"3'-(S-cysteinyl)-tyrosine (Tyr-Cys)","evidences":[{"source":"PubMed","id":"19393666","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"22281743","evidenceCode":"ECO:0000269"}]} |
| Chain | Residue | Details |
