3D1I
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite
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 | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 526 |
| Chain | Residue |
| A | GLU302 |
| A | TYR303 |
| A | LYS358 |
| A | GLN360 |
| A | HOH1232 |
| A | HOH1233 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 527 |
| Chain | Residue |
| A | HOH1048 |
| A | HOH1327 |
| A | HOH1386 |
| A | PRO116 |
| A | HEC1006 |
| A | HEC1007 |
| site_id | AC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO2 A 528 |
| Chain | Residue |
| A | ARG131 |
| A | TYR303 |
| A | HIS361 |
| A | HEC1004 |
| A | HOH1013 |
| A | HOH1359 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NA A 529 |
| Chain | Residue |
| A | HOH1404 |
| A | HOH1404 |
| A | HOH1404 |
| A | HOH1405 |
| A | HOH1405 |
| A | HOH1405 |
| site_id | AC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 526 |
| Chain | Residue |
| B | GLU302 |
| B | TYR303 |
| B | LYS358 |
| B | GLN360 |
| B | HOH1696 |
| B | HOH1697 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA B 527 |
| Chain | Residue |
| B | PRO116 |
| B | HEC1006 |
| B | HEC1007 |
| B | HOH1512 |
| B | HOH1789 |
| B | HOH1845 |
| B | HOH2002 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NO2 B 528 |
| Chain | Residue |
| B | ARG131 |
| B | TYR303 |
| B | HIS361 |
| B | HEC1004 |
| B | HOH1431 |
| B | HOH1818 |
| site_id | AC8 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE NA B 529 |
| Chain | Residue |
| B | HOH1863 |
| B | HOH1863 |
| B | HOH1863 |
| B | HOH1864 |
| B | HOH1864 |
| B | HOH1864 |
| B | HOH1994 |
| B | HOH1994 |
| B | HOH1994 |
| site_id | AC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC A 1004 |
| Chain | Residue |
| A | HIS113 |
| A | ALA114 |
| A | ASP125 |
| A | HIS126 |
| A | VAL129 |
| A | ARG131 |
| A | CYS184 |
| A | CYS187 |
| A | LYS188 |
| A | ARG242 |
| A | CYS299 |
| A | HIS300 |
| A | TYR303 |
| A | CYS305 |
| A | HIS361 |
| A | ASN486 |
| A | NO2528 |
| A | HEC1006 |
| A | HOH1013 |
| A | HOH1028 |
| A | HOH1145 |
| A | HOH1146 |
| A | HOH1152 |
| A | HOH1362 |
| site_id | BC1 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC A 1005 |
| Chain | Residue |
| A | CYS66 |
| A | HIS70 |
| A | GLN73 |
| A | PHE74 |
| A | LEU225 |
| A | CYS227 |
| A | CYS230 |
| A | HIS231 |
| A | ALA290 |
| A | MET384 |
| A | LYS386 |
| A | TYR395 |
| A | THR396 |
| A | HIS398 |
| A | HEC1003 |
| A | HOH1116 |
| A | HOH1229 |
| A | HOH1250 |
| A | HOH1445 |
| A | HOH1523 |
| A | HOH1531 |
| site_id | BC2 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC A 1006 |
| Chain | Residue |
| 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 | CA527 |
| A | HEC1004 |
| A | HEC1007 |
| A | HOH1017 |
| A | HOH1035 |
| A | HOH1140 |
| A | SER84 |
| A | PRO116 |
| site_id | BC3 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE HEC A 1007 |
| Chain | Residue |
| A | HIS300 |
| A | PHE367 |
| A | HIS372 |
| A | ALA378 |
| A | CYS379 |
| A | CYS382 |
| A | HIS383 |
| A | THR402 |
| A | PRO403 |
| A | ARG404 |
| A | ILE427 |
| A | LYS431 |
| A | ASN486 |
| A | PHE490 |
| A | HIS491 |
| A | CA527 |
| A | HEC1006 |
| A | HOH1140 |
| A | HOH1141 |
| A | HOH1149 |
| A | HOH1153 |
| A | HOH1327 |
| A | HOH1353 |
| site_id | BC4 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HEC A 1008 |
| Chain | Residue |
| A | ASN141 |
| A | TRP142 |
| A | GLN143 |
| A | VAL371 |
| A | HIS372 |
| A | ASN375 |
| A | PRO403 |
| A | ALA410 |
| A | CYS411 |
| A | CYS414 |
| A | HIS415 |
| A | TRP418 |
| A | ILE427 |
| A | PHE490 |
| A | HOH1413 |
| A | HOH1459 |
| A | HOH1461 |
| site_id | BC5 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC A 1002 |
| Chain | Residue |
| A | CYS14 |
| A | PHE15 |
| A | HIS18 |
| A | HIS25 |
| A | VAL33 |
| A | ASN34 |
| A | CYS35 |
| A | CYS38 |
| A | HIS39 |
| A | THR59 |
| A | ILE193 |
| A | LEU194 |
| A | PHE228 |
| A | PRO233 |
| A | HIS234 |
| A | ARG239 |
| A | PHE274 |
| A | ARG276 |
| A | ARG282 |
| A | HEC1001 |
| A | HEC1003 |
| A | HOH1087 |
| A | HOH1335 |
| A | HOH1471 |
| site_id | BC6 |
| Number of Residues | 21 |
| 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 | CYS227 |
| A | HIS231 |
| A | ALA236 |
| A | HEC1002 |
| A | HEC1005 |
| A | HOH1304 |
| A | HOH1347 |
| A | HOH1388 |
| A | HOH1434 |
| A | HOH1546 |
| A | HOH1567 |
| B | THR68 |
| B | HOH1472 |
| site_id | BC7 |
| Number of Residues | 22 |
| 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 | MET53 |
| A | ARG56 |
| A | PRO57 |
| A | THR59 |
| A | LEU194 |
| A | ARG276 |
| A | GLY277 |
| A | HEC1002 |
| A | HOH1089 |
| A | HOH1114 |
| A | HOH1470 |
| A | HOH1472 |
| site_id | BC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PG4 A 1009 |
| Chain | Residue |
| A | LYS431 |
| A | HIS435 |
| A | HOH1408 |
| A | HOH1446 |
| site_id | BC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PG6 A 1010 |
| Chain | Residue |
| A | TYR309 |
| A | LEU311 |
| A | GLY314 |
| A | ARG348 |
| A | ALA355 |
| A | HOH1247 |
| A | HOH1298 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 A 1011 |
| Chain | Residue |
| A | GLN138 |
| A | PHE139 |
| A | HOH1273 |
| A | HOH1536 |
| A | HOH1537 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 1012 |
| Chain | Residue |
| A | ARG153 |
| A | THR157 |
| A | ASN222 |
| site_id | CC3 |
| Number of Residues | 25 |
| 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 | VAL301 |
| B | TYR303 |
| B | CYS305 |
| B | HIS361 |
| B | ASN486 |
| B | NO2528 |
| B | HEC1006 |
| B | HOH1431 |
| B | HOH1492 |
| B | HOH1609 |
| B | HOH1610 |
| B | HOH1616 |
| B | HOH1940 |
| site_id | CC4 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC B 1005 |
| Chain | Residue |
| B | CYS66 |
| B | HIS70 |
| B | GLN73 |
| B | LEU225 |
| B | ASN226 |
| B | CYS227 |
| B | CYS230 |
| B | HIS231 |
| B | ALA290 |
| B | MET384 |
| B | LYS386 |
| B | TYR395 |
| B | THR396 |
| B | HIS398 |
| B | HEC1003 |
| B | HEC1006 |
| B | HOH1580 |
| B | HOH1693 |
| B | HOH1714 |
| B | HOH1904 |
| B | HOH1968 |
| site_id | CC5 |
| Number of Residues | 23 |
| 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 | LYS188 |
| B | MET229 |
| B | CYS296 |
| B | CYS299 |
| B | HIS300 |
| B | HIS383 |
| B | MET384 |
| B | CA527 |
| B | HEC1004 |
| B | HEC1005 |
| B | HEC1007 |
| B | HOH1481 |
| B | HOH1499 |
| B | HOH1604 |
| B | HOH2002 |
| site_id | CC6 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC B 1007 |
| Chain | Residue |
| B | HIS300 |
| B | PHE367 |
| B | HIS372 |
| B | ALA378 |
| B | CYS379 |
| B | CYS382 |
| B | HIS383 |
| B | THR402 |
| B | PRO403 |
| B | ARG404 |
| B | ILE427 |
| B | LYS431 |
| B | ASN486 |
| B | PHE490 |
| B | HIS491 |
| B | CA527 |
| B | HEC1006 |
| B | HOH1604 |
| B | HOH1605 |
| B | HOH1613 |
| B | HOH1617 |
| B | HOH1789 |
| B | HOH1812 |
| B | HOH2002 |
| site_id | CC7 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HEC B 1008 |
| Chain | Residue |
| B | ASN141 |
| B | TRP142 |
| B | GLN143 |
| B | VAL371 |
| B | HIS372 |
| B | ASN375 |
| B | PRO403 |
| B | ALA410 |
| B | CYS411 |
| B | CYS414 |
| B | HIS415 |
| B | TRP418 |
| B | ILE427 |
| B | PG41012 |
| B | HOH1872 |
| B | HOH1924 |
| B | HOH1954 |
| site_id | CC8 |
| 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 | HEC1001 |
| B | HEC1003 |
| B | HOH1551 |
| B | HOH1796 |
| site_id | CC9 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE HEC B 1003 |
| Chain | Residue |
| A | THR68 |
| B | LYS29 |
| B | HIS30 |
| B | VAL33 |
| B | HIS37 |
| B | ALA65 |
| B | CYS66 |
| B | CYS69 |
| B | HIS70 |
| B | CYS227 |
| B | HIS231 |
| B | ALA236 |
| B | HEC1002 |
| B | HEC1005 |
| B | HOH1440 |
| B | HOH1767 |
| B | HOH1807 |
| B | HOH1847 |
| B | HOH1893 |
| B | HOH1928 |
| site_id | DC1 |
| Number of Residues | 28 |
| Details | BINDING SITE FOR RESIDUE HEC B 1001 |
| Chain | Residue |
| B | GLN13 |
| B | CYS14 |
| B | CYS17 |
| B | HIS18 |
| B | HIS39 |
| B | ALA41 |
| B | HIS44 |
| B | VAL45 |
| B | ALA48 |
| B | SER49 |
| B | SER50 |
| B | ARG51 |
| B | ARG51 |
| B | ARG52 |
| B | MET53 |
| B | ARG56 |
| B | PRO57 |
| B | THR59 |
| B | LEU194 |
| B | GLN275 |
| B | ARG276 |
| B | HEC1002 |
| B | HOH1553 |
| B | HOH1578 |
| B | HOH1796 |
| B | HOH1912 |
| B | HOH1916 |
| B | HOH1932 |
| site_id | DC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 B 1009 |
| Chain | Residue |
| B | THR94 |
| B | THR94 |
| B | HIS435 |
| B | HOH1867 |
| B | HOH1905 |
| site_id | DC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE PG6 B 1010 |
| Chain | Residue |
| B | LEU311 |
| B | ASP313 |
| B | GLY314 |
| B | ARG348 |
| B | ALA355 |
| B | HOH1711 |
| B | HOH1934 |
| B | HOH1935 |
| site_id | DC4 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PG4 B 1011 |
| Chain | Residue |
| B | PHE172 |
| site_id | DC5 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PG4 B 1012 |
| Chain | Residue |
| B | TRP142 |
| B | PHE367 |
| B | SER370 |
| B | VAL371 |
| B | HIS372 |
| B | PHE490 |
| B | HIS491 |
| B | ASN492 |
| B | PRO493 |
| B | ASP494 |
| B | HEC1008 |
| B | HOH1963 |
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 |
