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 | 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 | 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: 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 |