2ZO5
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with azide
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005509 | molecular_function | calcium ion binding |
A | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
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 | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
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 | 25 |
Details | BINDING SITE FOR RESIDUE HEC A 1004 |
Chain | Residue |
A | HIS113 |
A | ARG242 |
A | CYS299 |
A | HIS300 |
A | TYR303 |
A | CYS305 |
A | HIS361 |
A | ASN486 |
A | AZI526 |
A | HEC1006 |
A | HOH1014 |
A | ALA114 |
A | HOH1029 |
A | HOH1149 |
A | HOH1150 |
A | HOH1156 |
A | HOH1165 |
A | HOH1377 |
A | ASP125 |
A | HIS126 |
A | VAL129 |
A | ARG131 |
A | CYS184 |
A | CYS187 |
A | LYS188 |
site_id | AC2 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEC A 1005 |
Chain | Residue |
A | CYS66 |
A | HIS70 |
A | GLN73 |
A | LEU225 |
A | CYS227 |
A | CYS230 |
A | HIS231 |
A | ALA290 |
A | MET384 |
A | TYR395 |
A | THR396 |
A | HIS398 |
A | HEC1003 |
A | HOH1122 |
A | HOH1234 |
A | HOH1255 |
A | HOH1289 |
A | HOH1535 |
site_id | AC3 |
Number of Residues | 21 |
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 | MET229 |
A | CYS296 |
A | CYS299 |
A | HIS300 |
A | HIS383 |
A | MET384 |
A | CA528 |
A | HEC1004 |
A | HEC1007 |
A | HOH1018 |
A | HOH1036 |
A | HOH1144 |
site_id | AC4 |
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 | CA528 |
A | HEC1006 |
A | HOH1144 |
A | HOH1145 |
A | HOH1153 |
A | HOH1157 |
A | HOH1336 |
A | HOH1364 |
site_id | AC5 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEC A 1008 |
Chain | Residue |
A | PHE490 |
A | HOH1423 |
A | HOH1461 |
A | HOH1463 |
A | HOH1529 |
A | ASN141 |
A | TRP142 |
A | GLN143 |
A | VAL371 |
A | HIS372 |
A | PRO403 |
A | ALA410 |
A | CYS411 |
A | CYS414 |
A | HIS415 |
A | TRP418 |
A | ILE427 |
site_id | AC6 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE HEC A 1002 |
Chain | Residue |
A | CYS14 |
A | PHE15 |
A | HIS18 |
A | VAL33 |
A | ASN34 |
A | CYS35 |
A | CYS38 |
A | HIS39 |
A | THR59 |
A | LEU194 |
A | PHE228 |
A | PRO233 |
A | HIS234 |
A | ARG239 |
A | PHE274 |
A | ARG276 |
A | ARG282 |
A | HEC1001 |
A | HEC1003 |
A | HOH1089 |
A | HOH1346 |
A | HOH1475 |
site_id | AC7 |
Number of Residues | 20 |
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 | HOH1120 |
A | HOH1314 |
A | HOH1359 |
A | HOH1398 |
A | HOH1439 |
A | HOH1550 |
B | THR68 |
site_id | AC8 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE HEC A 1001 |
Chain | Residue |
A | GLN13 |
A | CYS14 |
A | CYS17 |
A | HIS18 |
A | HIS39 |
A | HIS44 |
A | VAL45 |
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 | HOH1092 |
A | HOH1119 |
A | HOH1474 |
A | HOH1476 |
site_id | AC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE AZI A 526 |
Chain | Residue |
A | ARG131 |
A | TYR303 |
A | GLN360 |
A | HIS361 |
A | HEC1004 |
A | HOH1014 |
A | HOH1369 |
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 | HOH1237 |
A | HOH1238 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA A 528 |
Chain | Residue |
A | PRO116 |
A | HEC1006 |
A | HEC1007 |
A | HOH1049 |
A | HOH1336 |
A | HOH1396 |
site_id | BC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE NA A 529 |
Chain | Residue |
A | ASP450 |
A | HOH1415 |
A | HOH1415 |
A | HOH1415 |
A | HOH1416 |
A | HOH1416 |
A | HOH1416 |
site_id | BC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PG4 A 1009 |
Chain | Residue |
A | THR94 |
A | SER95 |
A | LYS431 |
A | HIS435 |
A | HOH1288 |
A | HOH1544 |
site_id | BC5 |
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 | HOH1252 |
A | HOH1307 |
site_id | BC6 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PG4 A 1011 |
Chain | Residue |
A | GLN138 |
A | PHE139 |
A | ASN141 |
A | TRP142 |
A | ASP494 |
A | HOH1362 |
site_id | BC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE TRS A 1012 |
Chain | Residue |
A | MET99 |
A | MET99 |
A | LYS102 |
A | LYS102 |
A | LYS102 |
A | AZI530 |
A | AZI530 |
A | HOH1052 |
A | HOH1052 |
A | HOH1328 |
A | HOH1328 |
A | HOH1328 |
A | HOH1415 |
A | HOH1415 |
A | HOH1415 |
site_id | BC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE AZI A 530 |
Chain | Residue |
A | PRO98 |
A | TRS1012 |
A | TRS1012 |
A | HOH1046 |
A | HOH1290 |
A | HOH1394 |
site_id | BC9 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PG4 A 1013 |
Chain | Residue |
A | MET12 |
A | ALA31 |
A | THR32 |
A | ASN34 |
A | HOH1335 |
B | PRO8 |
B | VAL9 |
B | PG41009 |
site_id | CC1 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE HEC B 1004 |
Chain | Residue |
B | HIS113 |
B | ALA114 |
B | ASP125 |
B | HIS126 |
B | VAL129 |
B | ARG131 |
B | ALA179 |
B | CYS184 |
B | CYS187 |
B | LYS188 |
B | ARG242 |
B | CYS299 |
B | HIS300 |
B | VAL301 |
B | TYR303 |
B | CYS305 |
B | HIS361 |
B | ASN486 |
B | AZI526 |
B | HEC1006 |
B | HOH1039 |
B | HOH1090 |
B | HOH1210 |
B | HOH1211 |
B | HOH1217 |
B | HOH1437 |
site_id | CC2 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC B 1005 |
Chain | Residue |
B | CYS66 |
B | HIS70 |
B | GLN73 |
B | PHE74 |
B | LEU225 |
B | ASN226 |
B | CYS227 |
B | CYS230 |
B | HIS231 |
B | ALA290 |
B | MET384 |
B | TYR395 |
B | THR396 |
B | HIS398 |
B | HEC1003 |
B | HEC1006 |
B | HOH1183 |
B | HOH1295 |
B | HOH1316 |
B | HOH1350 |
B | HOH1595 |
site_id | CC3 |
Number of Residues | 21 |
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 | CA528 |
B | HEC1004 |
B | HEC1005 |
B | HEC1007 |
B | HOH1079 |
B | HOH1097 |
B | HOH1205 |
site_id | CC4 |
Number of Residues | 22 |
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 | LYS431 |
B | ASN486 |
B | PHE490 |
B | HIS491 |
B | CA528 |
B | HEC1006 |
B | HOH1205 |
B | HOH1206 |
B | HOH1214 |
B | HOH1218 |
B | HOH1397 |
B | HOH1424 |
site_id | CC5 |
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 | PRO403 |
B | ALA410 |
B | CYS411 |
B | CYS414 |
B | HIS415 |
B | TRP418 |
B | ILE427 |
B | PHE490 |
B | PG41016 |
B | HOH1483 |
B | HOH1530 |
B | HOH1556 |
site_id | CC6 |
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 | HOH1150 |
B | HOH1407 |
site_id | CC7 |
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 | HEC1002 |
B | HEC1005 |
B | HOH1180 |
B | HOH1375 |
B | HOH1419 |
B | HOH1458 |
B | HOH1594 |
site_id | CC8 |
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 | HOH1153 |
B | HOH1179 |
B | HOH1407 |
B | HOH1517 |
B | HOH1522 |
B | HOH1538 |
site_id | CC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PG4 B 1009 |
Chain | Residue |
A | THR32 |
A | PG41013 |
A | HOH1534 |
B | ALA31 |
B | THR32 |
B | ASN34 |
B | HOH1396 |
site_id | DC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE AZI B 526 |
Chain | Residue |
B | ARG131 |
B | TYR303 |
B | GLN360 |
B | HIS361 |
B | HEC1004 |
B | HOH1039 |
B | HOH1429 |
B | HOH1437 |
site_id | DC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA B 527 |
Chain | Residue |
B | GLU302 |
B | TYR303 |
B | LYS358 |
B | GLN360 |
B | HOH1298 |
B | HOH1299 |
site_id | DC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA B 528 |
Chain | Residue |
B | PRO116 |
B | HEC1006 |
B | HEC1007 |
B | PG41014 |
B | HOH1110 |
B | HOH1397 |
B | HOH1456 |
site_id | DC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE NA B 529 |
Chain | Residue |
B | ASP450 |
B | HOH1475 |
B | HOH1475 |
B | HOH1475 |
B | HOH1476 |
B | HOH1476 |
site_id | DC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE PG4 B 1010 |
Chain | Residue |
B | THR94 |
B | LYS431 |
B | HIS435 |
B | HOH1478 |
B | HOH1535 |
B | HOH1607 |
site_id | DC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PG6 B 1011 |
Chain | Residue |
B | TYR309 |
B | LEU311 |
B | GLY314 |
B | ARG348 |
B | ALA355 |
B | HOH1313 |
B | HOH1368 |
site_id | DC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE TRS B 1012 |
Chain | Residue |
B | MET99 |
B | MET99 |
B | LYS102 |
B | LYS102 |
B | AZI530 |
B | AZI530 |
B | HOH1113 |
B | HOH1113 |
B | HOH1389 |
B | HOH1389 |
B | HOH1389 |
B | HOH1475 |
B | HOH1475 |
B | HOH1612 |
B | HOH1612 |
site_id | DC8 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE PG4 B 1013 |
Chain | Residue |
B | PHE172 |
B | SER174 |
site_id | DC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE AZI B 530 |
Chain | Residue |
B | PRO98 |
B | TRS1012 |
B | TRS1012 |
B | HOH1107 |
B | HOH1351 |
B | HOH1454 |
B | HOH1454 |
site_id | EC1 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE PG4 B 1014 |
Chain | Residue |
B | ARG81 |
B | GLU83 |
B | SER84 |
B | HIS85 |
B | GLU115 |
B | PRO116 |
B | CA528 |
B | HOH1206 |
B | HOH1367 |
B | HOH1379 |
B | HOH1393 |
B | HOH1397 |
B | HOH1424 |
B | HOH1446 |
B | HOH1456 |
B | HOH1548 |
B | HOH1582 |
site_id | EC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE PG4 B 1015 |
Chain | Residue |
B | LEU311 |
B | LYS336 |
B | GLN340 |
B | GLU470 |
B | TYR473 |
B | HOH1325 |
B | HOH1581 |
site_id | EC3 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE PG4 B 1016 |
Chain | Residue |
B | SER370 |
B | VAL371 |
B | ASN492 |
B | PRO493 |
B | ASP494 |
B | HEC1008 |
B | HOH1104 |
B | HOH1566 |
site_id | EC4 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE PG4 B 1017 |
Chain | Residue |
B | ARG60 |
B | ASP62 |
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 | CYS66 | |
A | CYS69 | |
A | CYS184 | |
A | CYS187 | |
A | CYS227 | |
A | CYS230 | |
A | CYS296 | |
A | CYS299 | |
A | CYS379 | |
A | CYS382 | |
A | CYS411 | |
A | CYS414 | |
B | CYS14 | |
B | CYS17 | |
B | CYS35 | |
B | CYS38 | |
B | CYS66 | |
B | CYS69 | |
B | CYS184 | |
B | CYS187 | |
B | CYS227 | |
B | CYS230 | |
B | CYS296 | |
B | CYS299 | |
B | CYS379 | |
B | CYS382 | |
B | CYS411 | |
B | CYS414 | |
A | CYS14 | |
A | CYS17 | |
A | CYS35 | |
A | CYS38 |
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 | HIS70 | |
A | HIS119 | |
A | LYS188 | |
A | HIS234 | |
A | HIS300 | |
A | HIS372 | |
A | HIS383 | |
A | HIS398 | |
A | HIS415 | |
A | HIS491 | |
B | HIS18 | |
B | HIS30 | |
B | HIS39 | |
B | HIS44 | |
B | HIS70 | |
B | HIS119 | |
B | LYS188 | |
B | HIS234 | |
B | HIS300 | |
B | HIS372 | |
B | HIS383 | |
B | HIS398 | |
B | HIS415 | |
B | HIS491 | |
A | HIS18 | |
A | HIS30 | |
A | HIS39 | |
A | HIS44 |
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 |
B | GLU302 | |
B | TYR303 | |
B | LYS358 | |
B | GLN360 | |
A | GLU302 | |
A | TYR303 | |
A | LYS358 | |
A | 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 |
B | TYR303 | |
B | CYS305 | |
A | TYR303 | |
A | CYS305 |