2VR0
Crystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
A | 0042597 | cellular_component | periplasmic space |
B | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
B | 0042597 | cellular_component | periplasmic space |
C | 0005886 | cellular_component | plasma membrane |
C | 0009055 | molecular_function | electron transfer activity |
C | 0009061 | biological_process | anaerobic respiration |
C | 0016020 | cellular_component | membrane |
C | 0019333 | biological_process | denitrification pathway |
C | 0020037 | molecular_function | heme binding |
C | 0046872 | molecular_function | metal ion binding |
D | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
D | 0042597 | cellular_component | periplasmic space |
E | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
E | 0042597 | cellular_component | periplasmic space |
F | 0005886 | cellular_component | plasma membrane |
F | 0009055 | molecular_function | electron transfer activity |
F | 0009061 | biological_process | anaerobic respiration |
F | 0016020 | cellular_component | membrane |
F | 0019333 | biological_process | denitrification pathway |
F | 0020037 | molecular_function | heme binding |
F | 0046872 | molecular_function | metal ion binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE HEM A1001 |
Chain | Residue |
A | ARG116 |
A | TYR236 |
A | HIS298 |
A | ASN429 |
A | HEC1003 |
A | HOH2023 |
A | ALA118 |
A | ILE131 |
A | ARG133 |
A | CYS147 |
A | CYS150 |
A | LYS151 |
A | CYS232 |
A | HIS233 |
site_id | AC2 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEM A1002 |
Chain | Residue |
A | TYR39 |
A | PHE57 |
A | GLN60 |
A | TYR61 |
A | TYR64 |
A | GLY186 |
A | CYS187 |
A | CYS190 |
A | HIS191 |
A | MET196 |
A | LEU198 |
A | ARG221 |
A | ARG225 |
A | MET321 |
A | ILE332 |
A | SER333 |
A | HIS335 |
A | TRP337 |
A | HEC1003 |
C | GLU126 |
C | VAL127 |
site_id | AC3 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE HEM A1003 |
Chain | Residue |
A | GLY78 |
A | SER79 |
A | ALA118 |
A | ARG119 |
A | GLY120 |
A | HIS121 |
A | TYR123 |
A | ALA124 |
A | ASP127 |
A | CYS150 |
A | ILE185 |
A | THR189 |
A | VAL228 |
A | CYS229 |
A | CYS232 |
A | HIS233 |
A | HIS320 |
A | TRP337 |
A | THR338 |
A | HEC1001 |
A | HEC1002 |
A | HEC1004 |
A | CA1007 |
site_id | AC4 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEM A1004 |
Chain | Residue |
A | THR74 |
A | LYS77 |
A | GLY78 |
A | GLU117 |
A | HIS233 |
A | GLU300 |
A | TRP304 |
A | HIS309 |
A | VAL314 |
A | THR315 |
A | CYS316 |
A | CYS319 |
A | HIS320 |
A | SER339 |
A | MET341 |
A | GLN369 |
A | ASN429 |
A | PHE433 |
A | HIS434 |
A | HEC1003 |
A | CA1007 |
site_id | AC5 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE HEM A1005 |
Chain | Residue |
A | HIS309 |
A | CYS319 |
A | PRO340 |
A | MET346 |
A | CYS349 |
A | CYS352 |
A | HIS353 |
A | ARG364 |
B | HIS353 |
B | LYS356 |
B | HEC1005 |
C | ASP138 |
C | ARG141 |
site_id | AC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA A1006 |
Chain | Residue |
A | GLU235 |
A | TYR236 |
A | LYS295 |
A | GLN297 |
A | HOH2014 |
site_id | AC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA A1007 |
Chain | Residue |
A | ALA118 |
A | HEC1003 |
A | HEC1004 |
A | GLY78 |
A | GLU117 |
site_id | AC8 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEM B1001 |
Chain | Residue |
B | ARG116 |
B | ALA118 |
B | PHE128 |
B | ILE131 |
B | ARG133 |
B | CYS147 |
B | CYS150 |
B | LYS151 |
B | CYS232 |
B | HIS233 |
B | TYR236 |
B | PHE238 |
B | HIS298 |
B | ASN429 |
B | HEC1003 |
B | HOH2008 |
B | HOH2040 |
B | HOH2041 |
site_id | AC9 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE HEM B1002 |
Chain | Residue |
B | TYR39 |
B | PHE57 |
B | GLN60 |
B | TYR64 |
B | GLY186 |
B | CYS187 |
B | CYS190 |
B | HIS191 |
B | MET196 |
B | LEU198 |
B | ARG221 |
B | ARG225 |
B | MET321 |
B | TYR323 |
B | SER333 |
B | HIS335 |
B | TRP337 |
B | HEC1003 |
C | ALA157 |
site_id | BC1 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEM B1003 |
Chain | Residue |
B | GLY78 |
B | SER79 |
B | ALA118 |
B | ARG119 |
B | GLY120 |
B | HIS121 |
B | TYR123 |
B | ALA124 |
B | ASP127 |
B | CYS150 |
B | ILE185 |
B | VAL228 |
B | CYS229 |
B | CYS232 |
B | HIS233 |
B | HIS320 |
B | MET321 |
B | TRP337 |
B | THR338 |
B | HEC1001 |
B | HEC1002 |
B | HEC1004 |
B | CA1007 |
B | HOH2029 |
site_id | BC2 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE HEM B1004 |
Chain | Residue |
B | THR74 |
B | LYS77 |
B | GLY78 |
B | GLU117 |
B | ALA118 |
B | HIS233 |
B | GLU300 |
B | TRP304 |
B | HIS309 |
B | VAL314 |
B | THR315 |
B | CYS316 |
B | CYS319 |
B | HIS320 |
B | SER339 |
B | GLN369 |
B | ASN429 |
B | PHE433 |
B | HIS434 |
B | HEC1003 |
B | HEC1005 |
B | CA1007 |
B | HOH2029 |
site_id | BC3 |
Number of Residues | 16 |
Details | BINDING SITE FOR RESIDUE HEM B1005 |
Chain | Residue |
A | HIS353 |
A | LYS356 |
A | HEC1005 |
B | HIS309 |
B | VAL314 |
B | ASP318 |
B | PRO340 |
B | CYS349 |
B | CYS352 |
B | HIS353 |
B | ARG364 |
B | VAL365 |
B | PHE433 |
B | PRO436 |
B | HEC1004 |
C | MET148 |
site_id | BC4 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA B1006 |
Chain | Residue |
B | GLU235 |
B | TYR236 |
B | LYS295 |
B | GLN297 |
B | HOH2016 |
site_id | BC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA B1007 |
Chain | Residue |
B | GLY78 |
B | GLU117 |
B | ALA118 |
B | HEC1003 |
B | HEC1004 |
site_id | BC6 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE HEM C1001 |
Chain | Residue |
C | THR37 |
C | CYS43 |
C | CYS46 |
C | MET49 |
C | ASN67 |
C | ASP89 |
C | MET92 |
C | ASN93 |
C | ALA104 |
C | GLY105 |
C | THR108 |
C | HEC1002 |
C | HQO1005 |
site_id | BC7 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEM C1002 |
Chain | Residue |
C | ARG40 |
C | CYS43 |
C | MET49 |
C | VAL52 |
C | GLY53 |
C | HIS56 |
C | HIS61 |
C | SER65 |
C | CYS66 |
C | CYS69 |
C | HIS70 |
C | ILE102 |
C | ALA104 |
C | LYS109 |
C | THR137 |
C | GLN144 |
C | HIS145 |
C | HEC1001 |
site_id | BC8 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEM C1003 |
Chain | Residue |
C | GLY60 |
C | HIS61 |
C | ASP68 |
C | CYS69 |
C | ASN115 |
C | CYS116 |
C | CYS119 |
C | HIS120 |
C | HIS140 |
C | VAL143 |
C | HEC1004 |
D | LYS329 |
F | CYS119 |
F | HIS120 |
F | MET122 |
F | THR123 |
F | HEC1003 |
site_id | BC9 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEM C1004 |
Chain | Residue |
A | TYR323 |
A | THR324 |
A | ARG325 |
A | LYS331 |
A | ARG347 |
A | GLN351 |
C | CYS116 |
C | HIS120 |
C | ASN124 |
C | SER129 |
C | CYS136 |
C | CYS139 |
C | HIS140 |
C | HEC1003 |
D | ARG325 |
D | LYS329 |
F | HEC1004 |
site_id | CC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE HQO C1005 |
Chain | Residue |
C | MET34 |
C | PHE42 |
C | ASN67 |
C | LYS82 |
C | ALA85 |
C | GLY86 |
C | ASP89 |
C | HEC1001 |
site_id | CC2 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEM D1001 |
Chain | Residue |
D | TYR115 |
D | ARG116 |
D | ALA118 |
D | PHE128 |
D | ILE131 |
D | ARG133 |
D | CYS147 |
D | CYS150 |
D | LYS151 |
D | CYS232 |
D | HIS233 |
D | TYR236 |
D | HIS298 |
D | ASN429 |
D | HEC1003 |
D | HOH2007 |
D | HOH2019 |
D | HOH2020 |
site_id | CC3 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE HEM D1002 |
Chain | Residue |
D | TYR39 |
D | PHE57 |
D | GLN60 |
D | TYR61 |
D | TYR64 |
D | GLY186 |
D | CYS187 |
D | CYS190 |
D | HIS191 |
D | MET196 |
D | ARG221 |
D | ARG225 |
D | MET321 |
D | SER333 |
D | HIS335 |
D | TRP337 |
D | HEC1003 |
F | GLU126 |
F | VAL127 |
site_id | CC4 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE HEM D1003 |
Chain | Residue |
D | GLY78 |
D | SER79 |
D | ALA118 |
D | ARG119 |
D | GLY120 |
D | HIS121 |
D | TYR123 |
D | ALA124 |
D | ASP127 |
D | CYS150 |
D | LYS151 |
D | ILE185 |
D | THR189 |
D | VAL228 |
D | CYS229 |
D | CYS232 |
D | HIS233 |
D | HIS320 |
D | MET321 |
D | TRP337 |
D | THR338 |
D | HEC1001 |
D | HEC1002 |
D | HEC1004 |
D | CA1007 |
site_id | CC5 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEM D1004 |
Chain | Residue |
D | THR74 |
D | LYS77 |
D | GLY78 |
D | GLU117 |
D | HIS233 |
D | GLU300 |
D | TRP304 |
D | HIS309 |
D | VAL314 |
D | THR315 |
D | CYS316 |
D | CYS319 |
D | HIS320 |
D | SER339 |
D | GLN369 |
D | ASN429 |
D | PHE433 |
D | HIS434 |
D | HEC1003 |
D | HEC1005 |
D | CA1007 |
site_id | CC6 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE HEM D1005 |
Chain | Residue |
D | HIS309 |
D | VAL314 |
D | MET346 |
D | ALA348 |
D | CYS349 |
D | CYS352 |
D | HIS353 |
D | ARG364 |
D | HEC1004 |
E | HIS353 |
E | LYS356 |
F | ARG141 |
site_id | CC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA D1006 |
Chain | Residue |
D | GLU235 |
D | TYR236 |
D | ASP283 |
D | LYS295 |
D | GLN297 |
site_id | CC8 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA D1007 |
Chain | Residue |
D | GLY78 |
D | GLU117 |
D | ALA118 |
D | HEC1003 |
D | HEC1004 |
site_id | CC9 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEM E1001 |
Chain | Residue |
E | ARG116 |
E | ALA118 |
E | ASP127 |
E | ILE131 |
E | ARG133 |
E | CYS147 |
E | CYS150 |
E | LYS151 |
E | CYS232 |
E | HIS233 |
E | VAL234 |
E | TYR236 |
E | HIS298 |
E | ASN429 |
E | HEC1003 |
E | HOH2005 |
E | HOH2013 |
site_id | DC1 |
Number of Residues | 18 |
Details | BINDING SITE FOR RESIDUE HEM E1002 |
Chain | Residue |
E | TYR39 |
E | GLN60 |
E | TYR64 |
E | GLY186 |
E | CYS187 |
E | CYS190 |
E | HIS191 |
E | MET196 |
E | ARG221 |
E | ARG225 |
E | MET321 |
E | TYR323 |
E | ILE332 |
E | SER333 |
E | HIS335 |
E | TRP337 |
E | HEC1003 |
F | ALA157 |
site_id | DC2 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEM E1003 |
Chain | Residue |
E | GLY78 |
E | SER79 |
E | ALA118 |
E | ARG119 |
E | GLY120 |
E | HIS121 |
E | ALA124 |
E | ASP127 |
E | CYS150 |
E | LYS151 |
E | ILE185 |
E | THR189 |
E | VAL228 |
E | CYS229 |
E | CYS232 |
E | HIS233 |
E | HIS320 |
E | MET321 |
E | TRP337 |
E | THR338 |
E | HEC1001 |
E | HEC1002 |
E | HEC1004 |
E | CA1007 |
site_id | DC3 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE HEM E1004 |
Chain | Residue |
E | THR74 |
E | LYS77 |
E | GLY78 |
E | GLU117 |
E | GLU300 |
E | TRP304 |
E | HIS309 |
E | VAL314 |
E | THR315 |
E | CYS316 |
E | CYS319 |
E | HIS320 |
E | SER339 |
E | PRO340 |
E | MET341 |
E | GLN369 |
E | ASN429 |
E | PHE433 |
E | HIS434 |
E | HEC1003 |
E | CA1007 |
E | HOH2009 |
site_id | DC4 |
Number of Residues | 14 |
Details | BINDING SITE FOR RESIDUE HEM E1005 |
Chain | Residue |
D | HIS353 |
D | LYS356 |
E | HIS309 |
E | VAL314 |
E | ASP318 |
E | PRO340 |
E | CYS349 |
E | CYS352 |
E | HIS353 |
E | ARG364 |
E | VAL365 |
E | PRO436 |
E | HOH2014 |
F | MET148 |
site_id | DC5 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE CA E1006 |
Chain | Residue |
E | GLU235 |
E | TYR236 |
E | LYS295 |
E | GLN297 |
site_id | DC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA E1007 |
Chain | Residue |
E | GLY78 |
E | GLU117 |
E | ALA118 |
E | HEC1003 |
E | HEC1004 |
site_id | DC7 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE HEM F1001 |
Chain | Residue |
F | THR37 |
F | CYS43 |
F | CYS46 |
F | MET49 |
F | CYS66 |
F | ASN67 |
F | HIS70 |
F | ASP89 |
F | MET92 |
F | LEU103 |
F | ALA104 |
F | GLY105 |
F | THR108 |
F | HEC1002 |
F | HQO1005 |
site_id | DC8 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEM F1002 |
Chain | Residue |
F | ARG40 |
F | CYS43 |
F | MET49 |
F | VAL52 |
F | HIS56 |
F | HIS61 |
F | SER65 |
F | CYS66 |
F | CYS69 |
F | HIS70 |
F | ALA104 |
F | LYS109 |
F | THR137 |
F | VAL143 |
F | GLN144 |
F | HIS145 |
F | HEC1001 |
site_id | DC9 |
Number of Residues | 17 |
Details | BINDING SITE FOR RESIDUE HEM F1003 |
Chain | Residue |
A | LYS329 |
C | CYS119 |
C | HIS120 |
C | MET122 |
C | THR123 |
C | HEC1003 |
F | GLY60 |
F | HIS61 |
F | ASP68 |
F | CYS69 |
F | VAL112 |
F | ASN115 |
F | CYS116 |
F | CYS119 |
F | HIS120 |
F | HIS140 |
F | HOH2003 |
site_id | EC1 |
Number of Residues | 15 |
Details | BINDING SITE FOR RESIDUE HEM F1004 |
Chain | Residue |
A | ARG325 |
A | LYS329 |
C | HEC1004 |
D | TYR323 |
D | THR324 |
D | ARG325 |
D | LYS331 |
D | ARG347 |
D | GLN351 |
F | HIS120 |
F | ASN124 |
F | SER129 |
F | CYS136 |
F | CYS139 |
F | HIS140 |
site_id | EC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE HQO F1005 |
Chain | Residue |
F | THR37 |
F | ASN67 |
F | LYS82 |
F | ALA85 |
F | GLY86 |
F | ASP89 |
F | HEC1001 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 24 |
Details | TOPO_DOM: Cytoplasmic => ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779 |
Chain | Residue | Details |
C | SER2-LYS14 | |
B | ALA118 | |
B | GLU235 | |
B | TYR236 | |
B | LYS295 | |
B | GLN297 | |
D | GLY78 | |
D | GLU117 | |
D | ALA118 | |
D | GLU235 | |
D | TYR236 | |
F | SER2-LYS14 | |
D | LYS295 | |
D | GLN297 | |
E | GLY78 | |
E | GLU117 | |
E | ALA118 | |
E | GLU235 | |
E | TYR236 | |
E | LYS295 | |
E | GLN297 | |
A | ALA118 | |
A | GLU235 | |
A | TYR236 | |
A | LYS295 | |
A | GLN297 | |
B | GLY78 | |
B | GLU117 |
site_id | SWS_FT_FI2 |
Number of Residues | 36 |
Details | TRANSMEM: Helical; Signal-anchor for type II membrane protein => ECO:0000255, ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779 |
Chain | Residue | Details |
C | LEU15-GLY33 | |
B | HIS121 | |
B | LYS151 | |
B | HIS191 | |
B | HIS233 | |
B | HIS309 | |
B | HIS320 | |
B | HIS335 | |
B | HIS353 | |
B | HIS434 | |
D | HIS121 | |
F | LEU15-GLY33 | |
D | LYS151 | |
D | HIS191 | |
D | HIS233 | |
D | HIS309 | |
D | HIS320 | |
D | HIS335 | |
D | HIS353 | |
D | HIS434 | |
E | HIS121 | |
E | LYS151 | |
A | HIS191 | |
E | HIS191 | |
E | HIS233 | |
E | HIS309 | |
E | HIS320 | |
E | HIS335 | |
E | HIS353 | |
E | HIS434 | |
A | HIS233 | |
A | HIS309 | |
A | HIS320 | |
A | HIS335 | |
A | HIS353 | |
A | HIS434 |
site_id | SWS_FT_FI3 |
Number of Residues | 250 |
Details | TOPO_DOM: Periplasmic => ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779 |
Chain | Residue | Details |
C | MET34-GLU159 | |
D | CYS187 | |
D | CYS232 | |
D | CYS319 | |
E | CYS147 | |
E | CYS187 | |
E | CYS232 | |
E | CYS319 | |
F | MET34-GLU159 | |
A | CYS232 | |
A | CYS319 | |
B | CYS147 | |
B | CYS187 | |
B | CYS232 | |
B | CYS319 | |
D | CYS147 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: covalent => ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A, ECO:0007744|PDB:2VR0 |
Chain | Residue | Details |
C | CYS43 | |
B | CYS352 | |
D | CYS150 | |
D | CYS229 | |
D | CYS316 | |
D | CYS349 | |
D | CYS352 | |
E | CYS150 | |
E | CYS229 | |
E | CYS316 | |
E | CYS349 | |
C | CYS66 | |
E | CYS352 | |
C | CYS69 | |
C | CYS136 | |
F | CYS43 | |
F | CYS66 | |
F | CYS69 | |
F | CYS136 | |
B | CYS349 |
site_id | SWS_FT_FI5 |
Number of Residues | 8 |
Details | BINDING: covalent => ECO:0000269|PubMed:17139260, ECO:0007744|PDB:2J7A |
Chain | Residue | Details |
C | CYS46 | |
C | CYS116 | |
C | CYS119 | |
C | CYS139 | |
F | CYS46 | |
F | CYS116 | |
F | CYS119 | |
F | CYS139 |
site_id | SWS_FT_FI6 |
Number of Residues | 4 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:17139260, ECO:0007744|PDB:2J7A |
Chain | Residue | Details |
C | MET49 | |
C | ASP89 | |
F | MET49 | |
F | ASP89 |
site_id | SWS_FT_FI7 |
Number of Residues | 10 |
Details | BINDING: axial binding residue => ECO:0000269|PubMed:17139260, ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2J7A, ECO:0007744|PDB:2VR0 |
Chain | Residue | Details |
C | HIS61 | |
F | HIS145 | |
C | HIS70 | |
C | HIS120 | |
C | HIS140 | |
C | HIS145 | |
F | HIS61 | |
F | HIS70 | |
F | HIS120 | |
F | HIS140 |
site_id | SWS_FT_FI8 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0000269|PubMed:18597779, ECO:0007744|PDB:2VR0 |
Chain | Residue | Details |
C | ASN67 | |
C | LYS82 | |
F | ASN67 | |
F | LYS82 |
site_id | SWS_FT_FI9 |
Number of Residues | 6 |
Details | SITE: Interaction with NrfA => ECO:0000269|PubMed:17139260, ECO:0007744|PDB:2J7A |
Chain | Residue | Details |
C | ARG40 | |
C | LYS57 | |
C | ASN63 | |
F | ARG40 | |
F | LYS57 | |
F | ASN63 |