3SCE
Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)
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 | 23 |
| Details | BINDING SITE FOR RESIDUE HEC A 1004 |
| Chain | Residue |
| A | PO41 |
| A | LYS188 |
| A | ARG242 |
| A | CYS299 |
| A | HIS300 |
| A | TYR303 |
| A | CYS305 |
| A | HIS361 |
| A | ASN486 |
| A | HOH554 |
| A | HOH727 |
| A | HIS113 |
| A | HOH728 |
| A | HOH734 |
| A | HEC1006 |
| A | HOH1058 |
| A | ALA114 |
| A | ASP125 |
| A | HIS126 |
| A | VAL129 |
| A | ARG131 |
| A | CYS184 |
| A | CYS187 |
| site_id | AC2 |
| 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 | ASN226 |
| A | CYS227 |
| A | CYS230 |
| A | HIS231 |
| A | ALA290 |
| A | MET384 |
| A | TYR395 |
| A | THR396 |
| A | HIS398 |
| A | HOH675 |
| A | HOH700 |
| A | HOH804 |
| A | HOH827 |
| A | HOH875 |
| A | HOH941 |
| A | HEC1003 |
| site_id | AC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE HEC A 1006 |
| Chain | Residue |
| A | CA3 |
| A | SER84 |
| A | PRO116 |
| A | ARG117 |
| A | HIS119 |
| A | PHE121 |
| A | MET122 |
| A | ASP125 |
| A | CYS187 |
| A | MET229 |
| A | CYS296 |
| A | CYS299 |
| A | HIS300 |
| A | HIS383 |
| A | MET384 |
| A | HOH544 |
| A | HOH562 |
| A | HOH722 |
| A | HEC1004 |
| A | HEC1007 |
| site_id | AC4 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC A 1007 |
| Chain | Residue |
| A | CA3 |
| A | HIS300 |
| 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 | PG4533 |
| A | HOH722 |
| A | HOH723 |
| A | HOH731 |
| A | HOH735 |
| A | HOH888 |
| A | HEC1006 |
| site_id | AC5 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC A 1008 |
| Chain | Residue |
| A | PG4530 |
| A | HOH658 |
| A | HOH878 |
| A | HOH893 |
| A | HOH1060 |
| A | HOH1074 |
| A | HOH1086 |
| A | ASN141 |
| A | TRP142 |
| A | GLN143 |
| A | VAL371 |
| A | HIS372 |
| A | VAL377 |
| A | PRO403 |
| A | ALA410 |
| A | CYS411 |
| A | CYS414 |
| A | HIS415 |
| A | TRP418 |
| A | ILE427 |
| A | PHE490 |
| 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 | HOH578 |
| A | HOH647 |
| A | HOH892 |
| A | HEC1001 |
| A | HEC1003 |
| site_id | AC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC A 1003 |
| Chain | Residue |
| A | LYS29 |
| A | HIS30 |
| A | HIS37 |
| A | ALA65 |
| A | CYS66 |
| A | CYS69 |
| A | HIS70 |
| A | CYS227 |
| A | HIS231 |
| A | ALA236 |
| A | HOH643 |
| A | HOH875 |
| A | HOH990 |
| A | HEC1002 |
| A | HEC1005 |
| A | HOH1036 |
| A | HOH1038 |
| A | HOH1120 |
| A | HOH1129 |
| 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 | ALA48 |
| A | SER49 |
| A | SER50 |
| A | ARG52 |
| A | MET53 |
| A | ARG56 |
| A | PRO57 |
| A | THR59 |
| A | LEU194 |
| A | ARG276 |
| A | GLY277 |
| A | HOH576 |
| A | HOH648 |
| A | HOH650 |
| A | HOH698 |
| A | HEC1002 |
| A | HOH1030 |
| site_id | AC9 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PO4 A 1 |
| Chain | Residue |
| A | PHE109 |
| A | ARG131 |
| A | TYR303 |
| A | GLN360 |
| A | HIS361 |
| A | HOH734 |
| A | HOH925 |
| A | HEC1004 |
| A | HOH1058 |
| A | HOH1059 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 2 |
| Chain | Residue |
| A | GLU302 |
| A | TYR303 |
| A | LYS358 |
| A | GLN360 |
| A | HOH807 |
| A | HOH808 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 3 |
| Chain | Residue |
| A | PRO116 |
| A | HOH571 |
| A | HOH582 |
| A | HOH888 |
| A | HEC1006 |
| A | HEC1007 |
| site_id | BC3 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 4 |
| Chain | Residue |
| A | ARG171 |
| A | PHE172 |
| A | SER174 |
| site_id | BC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG6 A 524 |
| Chain | Residue |
| A | GLN138 |
| A | PHE139 |
| A | TRP142 |
| A | ASP494 |
| A | HOH939 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG6 A 525 |
| Chain | Residue |
| A | LEU311 |
| A | GLY314 |
| A | ARG348 |
| A | ALA355 |
| A | HOH822 |
| site_id | BC6 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 526 |
| Chain | Residue |
| A | ARG60 |
| A | ASP62 |
| A | HOH653 |
| site_id | BC7 |
| Number of Residues | 12 |
| Details | BINDING SITE FOR RESIDUE PO4 A 527 |
| Chain | Residue |
| A | HOH585 |
| A | HOH585 |
| A | HOH585 |
| A | HOH901 |
| A | HOH901 |
| A | HOH901 |
| A | HOH913 |
| A | HOH913 |
| A | HOH913 |
| A | HOH950 |
| A | HOH950 |
| A | HOH950 |
| site_id | BC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 A 528 |
| Chain | Residue |
| A | LEU88 |
| A | ASN432 |
| A | HIS435 |
| A | HOH959 |
| A | HOH970 |
| site_id | BC9 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE PG4 A 529 |
| Chain | Residue |
| A | THR270 |
| site_id | CC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 530 |
| Chain | Residue |
| A | ASN375 |
| A | GLY376 |
| A | HEC1008 |
| site_id | CC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 531 |
| Chain | Residue |
| A | MET53 |
| A | GLU55 |
| A | ARG56 |
| site_id | CC3 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PG4 A 532 |
| Chain | Residue |
| A | ARG153 |
| A | HOH606 |
| site_id | CC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 A 533 |
| Chain | Residue |
| A | ARG81 |
| A | ARG404 |
| A | LYS431 |
| A | HEC1007 |
| A | HOH1061 |
| site_id | CC5 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE NA A 534 |
| Chain | Residue |
| A | GLU390 |
| A | HOH1047 |
| A | HOH1130 |
| B | HOH1027 |
| site_id | CC6 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA A 535 |
| Chain | Residue |
| A | GLU265 |
| A | ASP288 |
| A | HOH897 |
| A | HOH1077 |
| A | HOH1108 |
| site_id | CC7 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC B 1004 |
| Chain | Residue |
| B | PO41 |
| 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 | HOH667 |
| B | HOH788 |
| B | HOH789 |
| B | HOH795 |
| B | HEC1006 |
| B | HOH1114 |
| site_id | CC8 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE HEC B 1005 |
| Chain | Residue |
| B | CYS66 |
| B | HIS70 |
| B | GLN73 |
| B | PHE74 |
| B | LEU225 |
| B | CYS227 |
| B | CYS230 |
| B | HIS231 |
| B | ALA290 |
| B | MET384 |
| B | TYR395 |
| B | THR396 |
| B | HIS398 |
| B | HOH761 |
| B | HOH865 |
| B | HOH888 |
| B | HOH933 |
| B | HOH997 |
| B | HEC1003 |
| B | HEC1006 |
| site_id | CC9 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC B 1006 |
| Chain | Residue |
| B | CA3 |
| 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 | HOH637 |
| B | HOH675 |
| B | HOH783 |
| B | HEC1004 |
| B | HEC1005 |
| B | HEC1007 |
| site_id | DC1 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC B 1007 |
| Chain | Residue |
| B | CA3 |
| B | HIS300 |
| 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 | HOH545 |
| B | HOH783 |
| B | HOH784 |
| B | HOH792 |
| B | HOH796 |
| B | HOH944 |
| B | HEC1006 |
| site_id | DC2 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC B 1008 |
| Chain | Residue |
| B | ASN141 |
| B | TRP142 |
| B | GLN143 |
| B | VAL371 |
| B | HIS372 |
| B | ASN375 |
| B | VAL377 |
| B | PRO403 |
| B | ALA410 |
| B | CYS411 |
| B | CYS414 |
| B | HIS415 |
| B | TRP418 |
| B | ILE427 |
| B | PHE490 |
| B | PG4530 |
| B | HOH546 |
| B | HOH555 |
| B | HOH739 |
| B | HOH935 |
| B | HOH949 |
| B | HOH1116 |
| site_id | DC3 |
| 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 | HOH557 |
| B | HOH732 |
| B | HEC1001 |
| B | HEC1003 |
| site_id | DC4 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC B 1003 |
| Chain | Residue |
| B | LYS29 |
| B | HIS30 |
| B | VAL33 |
| B | HIS37 |
| B | ALA65 |
| B | CYS66 |
| B | CYS69 |
| B | HIS70 |
| B | CYS227 |
| B | HIS231 |
| B | ALA236 |
| B | HOH578 |
| B | HOH597 |
| B | HOH933 |
| B | HEC1002 |
| B | HEC1005 |
| B | HOH1055 |
| B | HOH1093 |
| B | HOH1095 |
| site_id | DC5 |
| Number of Residues | 26 |
| 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 | ARG52 |
| B | MET53 |
| B | ARG56 |
| B | PRO57 |
| B | THR59 |
| B | LEU194 |
| B | GLN275 |
| B | ARG276 |
| B | ARG278 |
| B | HOH557 |
| B | HOH560 |
| B | HOH734 |
| B | HOH759 |
| B | HOH902 |
| B | HEC1002 |
| B | HOH1039 |
| site_id | DC6 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE PO4 B 1 |
| Chain | Residue |
| B | PHE109 |
| B | ARG131 |
| B | TYR303 |
| B | GLN360 |
| B | HIS361 |
| B | HOH795 |
| B | HOH981 |
| B | HEC1004 |
| B | HOH1114 |
| B | HOH1115 |
| site_id | DC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 2 |
| Chain | Residue |
| B | GLU302 |
| B | TYR303 |
| B | LYS358 |
| B | GLN360 |
| B | HOH868 |
| B | HOH869 |
| site_id | DC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 3 |
| Chain | Residue |
| B | PRO116 |
| B | HOH688 |
| B | HOH698 |
| B | HOH944 |
| B | HEC1006 |
| B | HEC1007 |
| site_id | DC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 4 |
| Chain | Residue |
| B | ARG171 |
| B | PHE172 |
| B | SER174 |
| site_id | EC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG6 B 524 |
| Chain | Residue |
| B | GLN138 |
| B | PHE139 |
| B | TRP142 |
| site_id | EC2 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG6 B 525 |
| Chain | Residue |
| B | LEU311 |
| B | GLY314 |
| B | ARG348 |
| B | ALA355 |
| B | HOH883 |
| site_id | EC3 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE PO4 B 527 |
| Chain | Residue |
| B | HOH701 |
| B | HOH701 |
| B | HOH701 |
| B | HOH957 |
| B | HOH957 |
| B | HOH957 |
| B | HOH969 |
| B | HOH969 |
| B | HOH1014 |
| B | HOH1014 |
| B | HOH1014 |
| site_id | EC4 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PG4 B 528 |
| Chain | Residue |
| B | THR94 |
| B | HIS435 |
| site_id | EC5 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE PG4 B 529 |
| Chain | Residue |
| B | ALA110 |
| B | PHE111 |
| B | GLN175 |
| B | TRP444 |
| B | LYS508 |
| B | HOH672 |
| B | HOH695 |
| B | HOH703 |
| B | HOH910 |
| site_id | EC6 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PG4 B 530 |
| Chain | Residue |
| B | ASN375 |
| B | GLY376 |
| B | VAL377 |
| B | HEC1008 |
| site_id | EC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 B 531 |
| Chain | Residue |
| B | GLN267 |
| B | THR289 |
| B | ALA290 |
| B | HOH861 |
| B | HOH1044 |
| site_id | EC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PG4 B 532 |
| Chain | Residue |
| B | LEU311 |
| B | LYS336 |
| B | GLN340 |
| B | GLU470 |
| B | TYR473 |
| B | HOH898 |
| B | HOH899 |
| site_id | EC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 533 |
| Chain | Residue |
| B | ARG153 |
| B | THR157 |
| B | ASN222 |
| site_id | FC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 B 534 |
| Chain | Residue |
| B | LEU6 |
| B | VAL36 |
| B | HIS39 |
| B | ASP40 |
| B | ARG60 |
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 |
