2OT4
Structure of a hexameric multiheme c nitrite reductase from the extremophile bacterium Thiolkalivibrio nitratireducens
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 | 6 |
| Details | BINDING SITE FOR RESIDUE CA A 2744 |
| Chain | Residue |
| A | GLU302 |
| A | TYR303 |
| A | LYS358 |
| A | GLN360 |
| A | HOH3068 |
| A | HOH3069 |
| site_id | AC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA B 2333 |
| Chain | Residue |
| B | GLN360 |
| B | HOH2478 |
| B | HOH2479 |
| B | GLU302 |
| B | TYR303 |
| B | LYS358 |
| site_id | AC3 |
| Number of Residues | 20 |
| Details | BINDING SITE FOR RESIDUE HEC A 1004 |
| Chain | Residue |
| A | HIS113 |
| A | ALA114 |
| A | ASP125 |
| A | HIS126 |
| A | ARG131 |
| A | CYS184 |
| A | CYS187 |
| A | LYS188 |
| A | ARG242 |
| A | CYS299 |
| A | HIS300 |
| A | TYR303 |
| A | CYS305 |
| A | HIS361 |
| A | ASN486 |
| A | HOH2759 |
| A | HOH2950 |
| A | HOH2951 |
| A | HOH2958 |
| A | HOH2972 |
| site_id | AC4 |
| Number of Residues | 15 |
| 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 | MET384 |
| A | TYR395 |
| A | THR396 |
| A | HIS398 |
| A | HOH3065 |
| A | HOH3094 |
| A | HOH3326 |
| site_id | AC5 |
| Number of Residues | 20 |
| 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 | LEU225 |
| A | MET229 |
| A | CYS296 |
| A | CYS299 |
| A | HIS300 |
| A | HIS383 |
| A | MET384 |
| A | GLN400 |
| A | HOH2748 |
| A | HOH2767 |
| A | HOH2769 |
| A | HOH2944 |
| site_id | AC6 |
| Number of Residues | 19 |
| 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 | ARG404 |
| A | LYS431 |
| A | ASN486 |
| A | PHE490 |
| A | HIS491 |
| A | HOH2767 |
| A | HOH2944 |
| A | HOH2945 |
| A | HOH2946 |
| A | HOH2954 |
| A | HOH2959 |
| site_id | AC7 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE HEC A 1008 |
| Chain | Residue |
| A | PHE490 |
| A | HOH2866 |
| A | HOH2982 |
| A | ASN141 |
| A | TRP142 |
| A | GLN143 |
| A | HIS372 |
| A | ASN375 |
| A | PRO403 |
| A | ALA410 |
| A | CYS411 |
| A | CYS414 |
| A | HIS415 |
| A | TRP418 |
| A | ALA423 |
| A | ILE427 |
| site_id | AC8 |
| Number of Residues | 18 |
| Details | BINDING SITE FOR RESIDUE HEC A 1002 |
| Chain | Residue |
| A | CYS14 |
| A | PHE15 |
| A | HIS18 |
| A | ASN34 |
| A | CYS35 |
| A | CYS38 |
| A | HIS39 |
| A | LEU194 |
| A | PHE228 |
| A | PRO233 |
| A | HIS234 |
| A | ARG239 |
| A | PHE274 |
| A | ARG276 |
| A | ARG282 |
| A | HOH2853 |
| A | HOH2900 |
| A | HOH2922 |
| site_id | AC9 |
| 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 | CYS227 |
| A | HIS231 |
| A | ALA236 |
| A | HOH2906 |
| A | HOH3189 |
| A | HOH3193 |
| B | THR68 |
| site_id | BC1 |
| 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 | HOH2842 |
| A | HOH2856 |
| A | HOH2905 |
| A | HOH2920 |
| A | HOH3124 |
| site_id | BC2 |
| Number of Residues | 21 |
| Details | BINDING SITE FOR RESIDUE HEC B 1004 |
| Chain | Residue |
| B | HIS113 |
| B | ALA114 |
| B | ASP125 |
| B | HIS126 |
| 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 | HOH2363 |
| B | HOH2475 |
| B | HOH2608 |
| B | HOH2611 |
| B | HOH2765 |
| site_id | BC3 |
| Number of Residues | 16 |
| 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 | MET384 |
| B | TYR395 |
| B | THR396 |
| B | HIS398 |
| B | HOH2490 |
| B | HOH2671 |
| B | HOH2672 |
| B | HOH2926 |
| site_id | BC4 |
| Number of Residues | 18 |
| 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 | HOH2341 |
| B | HOH2351 |
| B | HOH2368 |
| B | HOH2585 |
| site_id | BC5 |
| Number of Residues | 19 |
| 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 | ARG404 |
| B | LYS431 |
| B | ASN486 |
| B | PHE490 |
| B | HIS491 |
| B | HOH2368 |
| B | HOH2474 |
| B | HOH2585 |
| B | HOH2587 |
| B | HOH2589 |
| B | HOH2610 |
| site_id | BC6 |
| Number of Residues | 16 |
| Details | BINDING SITE FOR RESIDUE HEC B 1008 |
| Chain | Residue |
| B | ASN141 |
| B | TRP142 |
| B | GLN143 |
| B | HIS372 |
| B | PRO403 |
| B | ALA410 |
| B | CYS411 |
| B | CYS414 |
| B | HIS415 |
| B | TRP418 |
| B | ALA423 |
| B | ILE427 |
| B | PHE490 |
| B | HOH2415 |
| B | HOH2749 |
| B | HOH2867 |
| site_id | BC7 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC B 1002 |
| Chain | Residue |
| B | CYS14 |
| B | PHE15 |
| B | HIS18 |
| B | ILE21 |
| B | HIS25 |
| 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 | HOH2563 |
| B | HOH2564 |
| site_id | BC8 |
| Number of Residues | 19 |
| Details | BINDING SITE FOR RESIDUE HEC B 1003 |
| Chain | Residue |
| A | THR68 |
| B | LYS29 |
| B | HIS30 |
| B | HIS37 |
| B | ALA65 |
| B | CYS66 |
| B | THR68 |
| B | CYS69 |
| B | HIS70 |
| B | CYS227 |
| B | HIS231 |
| B | ALA236 |
| B | HOH2566 |
| B | HOH2711 |
| B | HOH2712 |
| B | HOH2713 |
| B | HOH2781 |
| B | HOH2841 |
| B | HOH2914 |
| site_id | BC9 |
| Number of Residues | 24 |
| Details | BINDING SITE FOR RESIDUE HEC B 1001 |
| Chain | Residue |
| B | GLN13 |
| B | CYS14 |
| B | CYS17 |
| B | HIS18 |
| B | HIS39 |
| B | HIS44 |
| B | ALA48 |
| B | SER49 |
| B | SER50 |
| B | ARG51 |
| B | ARG52 |
| B | MET53 |
| B | ARG56 |
| B | PRO57 |
| B | THR59 |
| B | LEU194 |
| B | GLN275 |
| B | ARG276 |
| B | HOH2404 |
| B | HOH2431 |
| B | HOH2468 |
| B | HOH2487 |
| B | HOH2564 |
| B | HOH2573 |
| site_id | CC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE CIT B 2010 |
| Chain | Residue |
| B | SER49 |
| B | SER50 |
| B | ARG51 |
| B | HOH2877 |
| site_id | CC2 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE MRD B 2004 |
| Chain | Residue |
| A | PRO8 |
| A | HOH3269 |
| B | ALA11 |
| B | HIS25 |
| B | ALA31 |
| B | ASN34 |
| B | HOH2924 |
| site_id | CC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE MRD A 2005 |
| Chain | Residue |
| A | ALA11 |
| A | HIS25 |
| A | ALA31 |
| A | THR32 |
| A | ASN34 |
| A | HOH3269 |
| A | HOH3321 |
| A | HOH3345 |
| B | PRO8 |
| site_id | CC4 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE MRD A 2270 |
| Chain | Residue |
| A | THR59 |
| A | HOH3128 |
| A | HOH3313 |
| A | HOH3322 |
| site_id | CC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE MRD B 2288 |
| Chain | Residue |
| B | GLN310 |
| B | LEU311 |
| B | ASP313 |
| B | GLY314 |
| B | ARG348 |
| site_id | CC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MPD A 2001 |
| Chain | Residue |
| A | ARG87 |
| A | GLN138 |
| A | PHE139 |
| A | TRP142 |
| A | ARG497 |
| A | HOH3200 |
| site_id | CC7 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MPD B 2002 |
| Chain | Residue |
| B | ARG87 |
| B | GLN138 |
| B | PHE139 |
| B | TRP142 |
| B | ARG497 |
| B | HOH2849 |
| site_id | CC8 |
| Number of Residues | 3 |
| Details | BINDING SITE FOR RESIDUE MPD B 2040 |
| Chain | Residue |
| B | ASP23 |
| B | HOH2916 |
| B | HOH2925 |
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 |
