3UU9
Structure of the free TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase
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 601 |
| Chain | Residue |
| A | HIS113 |
| A | LYS188 |
| A | ARG242 |
| A | CYS299 |
| A | HIS300 |
| A | TYR303 |
| A | CYS305 |
| A | HIS361 |
| A | ASN486 |
| A | HEC603 |
| A | HOH715 |
| A | ALA114 |
| A | HOH756 |
| A | HOH759 |
| A | HOH788 |
| A | HOH1000 |
| A | ASP125 |
| A | HIS126 |
| A | VAL129 |
| A | ARG131 |
| A | ALA179 |
| A | CYS184 |
| A | CYS187 |
| site_id | AC2 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HEC A 602 |
| Chain | Residue |
| A | CYS66 |
| A | HIS70 |
| A | GLN73 |
| A | PHE74 |
| A | LEU225 |
| A | CYS227 |
| A | CYS230 |
| A | HIS231 |
| A | ALA290 |
| A | MET295 |
| A | MET384 |
| A | TYR395 |
| A | THR396 |
| A | HIS398 |
| A | HEC603 |
| A | HEC607 |
| A | HOH928 |
| site_id | AC3 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC A 603 |
| 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 | HEC601 |
| A | HEC602 |
| A | HEC604 |
| A | CA610 |
| A | HOH709 |
| A | HOH731 |
| A | HOH1048 |
| site_id | AC4 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE HEC A 604 |
| Chain | Residue |
| A | HIS300 |
| A | GLU363 |
| A | PHE367 |
| A | HIS372 |
| A | VAL377 |
| 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 | HEC603 |
| A | CA610 |
| A | HOH711 |
| A | HOH817 |
| A | HOH820 |
| A | HOH845 |
| A | HOH1043 |
| A | HOH1048 |
| site_id | AC5 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE HEC A 605 |
| Chain | Residue |
| A | ILE427 |
| A | PHE490 |
| A | HOH806 |
| A | HOH1006 |
| A | ASN141 |
| A | TRP142 |
| A | GLN143 |
| A | VAL371 |
| A | HIS372 |
| A | ASN375 |
| A | PRO403 |
| A | ALA410 |
| A | CYS411 |
| A | CYS414 |
| A | HIS415 |
| A | TRP418 |
| site_id | AC6 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC A 606 |
| Chain | Residue |
| A | CYS14 |
| A | PHE15 |
| A | HIS18 |
| A | ILE21 |
| A | HIS25 |
| A | VAL33 |
| A | ASN34 |
| A | CYS35 |
| A | CYS38 |
| A | HIS39 |
| A | ILE193 |
| A | LEU194 |
| A | PHE228 |
| A | PRO233 |
| A | HIS234 |
| A | ARG239 |
| A | PHE274 |
| A | ARG276 |
| A | ARG282 |
| A | HEC607 |
| A | HEC608 |
| A | HOH805 |
| A | HOH999 |
| A | HOH1060 |
| site_id | AC7 |
| Number of Residues | 17 |
| Details | BINDING SITE FOR RESIDUE HEC A 607 |
| Chain | Residue |
| A | LYS29 |
| A | HIS30 |
| A | VAL33 |
| A | HIS37 |
| A | ALA65 |
| A | CYS66 |
| A | CYS69 |
| A | HIS70 |
| A | CYS227 |
| A | HIS231 |
| A | ALA236 |
| A | HEC602 |
| A | HEC606 |
| A | HOH1035 |
| A | HOH1135 |
| B | HIS37 |
| B | THR68 |
| site_id | AC8 |
| Number of Residues | 22 |
| Details | BINDING SITE FOR RESIDUE HEC A 608 |
| Chain | Residue |
| A | GLN13 |
| A | CYS14 |
| A | CYS17 |
| A | HIS18 |
| A | HIS39 |
| A | ALA41 |
| A | HIS44 |
| A | VAL45 |
| A | ALA48 |
| A | SER49 |
| A | SER50 |
| A | ARG52 |
| A | ARG56 |
| A | PRO57 |
| A | THR59 |
| A | LEU194 |
| A | ARG276 |
| A | GLY277 |
| A | HEC606 |
| A | HOH814 |
| A | HOH819 |
| A | HOH1050 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 609 |
| Chain | Residue |
| A | GLU302 |
| A | TYR303 |
| A | LYS358 |
| A | GLN360 |
| A | HOH718 |
| A | HOH732 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 610 |
| Chain | Residue |
| A | PRO116 |
| A | HEC603 |
| A | HEC604 |
| A | HOH711 |
| A | HOH761 |
| A | HOH822 |
| site_id | BC2 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 611 |
| Chain | Residue |
| A | GLY314 |
| A | ARG348 |
| A | PG4612 |
| site_id | BC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE PG4 A 612 |
| Chain | Residue |
| A | LEU311 |
| A | GLY314 |
| A | ARG348 |
| A | ALA355 |
| A | PG4611 |
| A | HOH852 |
| site_id | BC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 A 613 |
| Chain | Residue |
| A | GLN138 |
| A | PHE139 |
| A | TRP142 |
| site_id | BC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PG4 A 614 |
| Chain | Residue |
| A | ARG171 |
| A | SER174 |
| site_id | BC6 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE HEC B 601 |
| 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 | TYR303 |
| B | CYS305 |
| B | HIS361 |
| B | ASN486 |
| B | HEC603 |
| B | HOH732 |
| B | HOH770 |
| B | HOH773 |
| B | HOH803 |
| B | HOH1012 |
| site_id | BC7 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE HEC B 602 |
| Chain | Residue |
| B | CYS66 |
| B | HIS70 |
| B | GLN73 |
| B | LEU225 |
| B | ASN226 |
| B | CYS227 |
| B | CYS230 |
| B | HIS231 |
| B | ALA290 |
| B | MET384 |
| B | TYR395 |
| B | THR396 |
| B | HIS398 |
| B | HEC603 |
| B | HEC607 |
| B | HOH862 |
| B | HOH942 |
| B | HOH1107 |
| site_id | BC8 |
| Number of Residues | 25 |
| Details | BINDING SITE FOR RESIDUE HEC B 603 |
| Chain | Residue |
| B | SER84 |
| B | PRO116 |
| B | ARG117 |
| B | HIS119 |
| B | PHE121 |
| B | MET122 |
| B | ASP125 |
| B | CYS187 |
| B | LYS188 |
| B | LEU225 |
| B | MET229 |
| B | MET295 |
| B | CYS296 |
| B | CYS299 |
| B | HIS300 |
| B | HIS383 |
| B | MET384 |
| B | GLN400 |
| B | HEC601 |
| B | HEC602 |
| B | HEC604 |
| B | CA610 |
| B | NA621 |
| B | HOH728 |
| B | HOH746 |
| site_id | BC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC B 604 |
| Chain | Residue |
| B | HIS300 |
| B | GLU363 |
| 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 | HEC603 |
| B | CA610 |
| B | NA621 |
| B | HOH729 |
| B | HOH832 |
| B | HOH835 |
| B | HOH860 |
| B | HOH1055 |
| site_id | CC1 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC B 605 |
| 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 | PHE490 |
| B | PG4616 |
| B | HOH821 |
| B | HOH1018 |
| B | HOH1100 |
| B | HOH1122 |
| site_id | CC2 |
| Number of Residues | 23 |
| Details | BINDING SITE FOR RESIDUE HEC B 606 |
| Chain | Residue |
| B | CYS14 |
| B | PHE15 |
| B | HIS18 |
| B | ILE21 |
| B | HIS25 |
| B | VAL33 |
| B | ASN34 |
| B | CYS35 |
| B | CYS38 |
| B | HIS39 |
| B | ILE193 |
| B | LEU194 |
| B | PHE228 |
| B | PRO233 |
| B | HIS234 |
| B | ARG239 |
| B | PHE274 |
| B | ARG276 |
| B | ARG282 |
| B | HEC607 |
| B | HEC608 |
| B | HOH820 |
| B | HOH1011 |
| site_id | CC3 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE HEC B 607 |
| Chain | Residue |
| A | HIS37 |
| B | LYS29 |
| B | HIS30 |
| B | HIS37 |
| B | ALA65 |
| B | CYS66 |
| B | CYS69 |
| B | HIS70 |
| B | CYS227 |
| B | HIS231 |
| B | ALA236 |
| B | HEC602 |
| B | HEC606 |
| B | HOH720 |
| B | HOH1047 |
| B | HOH1114 |
| B | HOH1115 |
| B | HOH1150 |
| site_id | CC4 |
| Number of Residues | 27 |
| Details | BINDING SITE FOR RESIDUE HEC B 608 |
| 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 | HEC606 |
| B | HOH829 |
| B | HOH834 |
| B | HOH945 |
| B | HOH1011 |
| B | HOH1079 |
| site_id | CC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 609 |
| Chain | Residue |
| B | GLU302 |
| B | TYR303 |
| B | LYS358 |
| B | GLN360 |
| B | HOH733 |
| B | HOH747 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 610 |
| Chain | Residue |
| B | PRO116 |
| B | HEC603 |
| B | HEC604 |
| B | HOH729 |
| B | HOH775 |
| B | HOH837 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 B 611 |
| Chain | Residue |
| B | LEU311 |
| B | ARG348 |
| B | ALA355 |
| B | PG4612 |
| B | HOH867 |
| site_id | CC8 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PG4 B 612 |
| Chain | Residue |
| B | GLY314 |
| B | ARG348 |
| B | PG4611 |
| B | HOH1076 |
| site_id | CC9 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 613 |
| Chain | Residue |
| B | GLN138 |
| B | PHE139 |
| B | TRP142 |
| site_id | DC1 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 614 |
| Chain | Residue |
| B | ARG171 |
| B | PHE172 |
| B | SER174 |
| site_id | DC2 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE PG4 B 615 |
| Chain | Residue |
| B | THR94 |
| B | SER95 |
| B | HIS435 |
| B | HOH703 |
| site_id | DC3 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE PG4 B 616 |
| Chain | Residue |
| B | ASN375 |
| B | GLY376 |
| B | ASP381 |
| B | CYS414 |
| B | HEC605 |
| site_id | DC4 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 617 |
| Chain | Residue |
| B | ARG153 |
| B | THR157 |
| B | HOH1034 |
| site_id | DC5 |
| Number of Residues | 2 |
| Details | BINDING SITE FOR RESIDUE PG4 B 618 |
| Chain | Residue |
| B | ARG374 |
| B | HOH933 |
| site_id | DC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE PG4 B 619 |
| Chain | Residue |
| B | HIS107 |
| B | GLY108 |
| B | ALA177 |
| B | THR178 |
| B | ALA179 |
| B | HOH1014 |
| B | HOH1073 |
| site_id | DC7 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE PG4 B 620 |
| Chain | Residue |
| B | PHE333 |
| B | LYS506 |
| B | HOH1070 |
| site_id | DC8 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NA B 621 |
| Chain | Residue |
| B | SER84 |
| B | ARG401 |
| B | THR402 |
| B | HEC603 |
| B | HEC604 |
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 |
