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 | 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 |
A | 0097164 | biological_process | ammonium ion metabolic process |
B | 0005509 | molecular_function | calcium ion binding |
B | 0016491 | molecular_function | oxidoreductase activity |
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 |
B | 0097164 | biological_process | ammonium ion metabolic process |
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: covalent => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | CYS14 | |
A | CYS230 | |
A | CYS296 | |
A | CYS299 | |
A | CYS379 | |
A | CYS382 | |
A | CYS411 | |
A | CYS414 | |
B | CYS14 | |
B | CYS17 | |
B | CYS35 | |
A | CYS17 | |
B | CYS38 | |
B | CYS66 | |
B | CYS69 | |
B | CYS184 | |
B | CYS187 | |
B | CYS227 | |
B | CYS230 | |
B | CYS296 | |
B | CYS299 | |
B | CYS379 | |
A | CYS35 | |
B | CYS382 | |
B | CYS411 | |
B | CYS414 | |
A | CYS38 | |
A | CYS66 | |
A | CYS69 | |
A | CYS184 | |
A | CYS187 | |
A | CYS227 |
site_id | SWS_FT_FI2 |
Number of Residues | 28 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | HIS18 | |
A | HIS372 | |
A | HIS383 | |
A | HIS398 | |
A | HIS415 | |
A | HIS491 | |
B | HIS18 | |
B | HIS30 | |
B | HIS39 | |
B | HIS44 | |
B | HIS70 | |
A | HIS30 | |
B | HIS119 | |
B | LYS188 | |
B | HIS234 | |
B | HIS300 | |
B | HIS372 | |
B | HIS383 | |
B | HIS398 | |
B | HIS415 | |
B | HIS491 | |
A | HIS39 | |
A | HIS44 | |
A | HIS70 | |
A | HIS119 | |
A | LYS188 | |
A | HIS234 | |
A | HIS300 |
site_id | SWS_FT_FI3 |
Number of Residues | 2 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743 |
Chain | Residue | Details |
A | HIS231 | |
B | HIS231 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y |
Chain | Residue | Details |
A | GLU302 | |
A | TYR303 | |
A | LYS358 | |
A | GLN360 | |
B | GLU302 | |
B | TYR303 | |
B | LYS358 | |
B | GLN360 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | CROSSLNK: 3'-(S-cysteinyl)-tyrosine (Tyr-Cys) => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:22281743 |
Chain | Residue | Details |
A | TYR303 | |
A | CYS305 | |
B | TYR303 | |
B | CYS305 |