3TOR
Crystal structure of Escherichia coli NrfA with Europium bound
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005506 | molecular_function | iron ion binding |
A | 0005509 | molecular_function | calcium ion binding |
A | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
A | 0009061 | biological_process | anaerobic respiration |
A | 0016491 | molecular_function | oxidoreductase activity |
A | 0016966 | molecular_function | nitric oxide reductase 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 |
B | 0005506 | molecular_function | iron ion binding |
B | 0005509 | molecular_function | calcium ion binding |
B | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
B | 0009061 | biological_process | anaerobic respiration |
B | 0016491 | molecular_function | oxidoreductase activity |
B | 0016966 | molecular_function | nitric oxide reductase 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 |
C | 0005506 | molecular_function | iron ion binding |
C | 0005509 | molecular_function | calcium ion binding |
C | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
C | 0009061 | biological_process | anaerobic respiration |
C | 0016491 | molecular_function | oxidoreductase activity |
C | 0016966 | molecular_function | nitric oxide reductase activity |
C | 0019645 | biological_process | anaerobic electron transport chain |
C | 0020037 | molecular_function | heme binding |
C | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
C | 0042128 | biological_process | nitrate assimilation |
C | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
C | 0042597 | cellular_component | periplasmic space |
C | 0046872 | molecular_function | metal ion binding |
D | 0005506 | molecular_function | iron ion binding |
D | 0005509 | molecular_function | calcium ion binding |
D | 0006807 | biological_process | obsolete nitrogen compound metabolic process |
D | 0009061 | biological_process | anaerobic respiration |
D | 0016491 | molecular_function | oxidoreductase activity |
D | 0016966 | molecular_function | nitric oxide reductase activity |
D | 0019645 | biological_process | anaerobic electron transport chain |
D | 0020037 | molecular_function | heme binding |
D | 0030288 | cellular_component | outer membrane-bounded periplasmic space |
D | 0042128 | biological_process | nitrate assimilation |
D | 0042279 | molecular_function | nitrite reductase (cytochrome, ammonia-forming) activity |
D | 0042597 | cellular_component | periplasmic space |
D | 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 1 |
Chain | Residue |
A | HOH21 |
A | GLU215 |
A | TYR216 |
A | LYS261 |
A | GLN263 |
A | HOH583 |
site_id | AC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE EU A 2 |
Chain | Residue |
A | HOH525 |
A | HOH626 |
A | HOH825 |
A | HOH854 |
A | HOH1993 |
A | HEC5 |
A | HEC6 |
A | PRO91 |
site_id | AC3 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC A 3 |
Chain | Residue |
A | HEC5 |
A | HOH10 |
A | HOH13 |
A | HOH24 |
A | TYR88 |
A | ASN89 |
A | PRO91 |
A | ASP100 |
A | THR104 |
A | ARG106 |
A | CYS122 |
A | CYS125 |
A | LYS126 |
A | CYS212 |
A | HIS213 |
A | TYR216 |
A | HIS264 |
A | HIS388 |
A | HOH487 |
A | HOH502 |
A | HOH518 |
A | HOH537 |
A | HOH577 |
A | HOH1316 |
site_id | AC4 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE HEC A 4 |
Chain | Residue |
A | HEC5 |
A | HIS49 |
A | GLN52 |
A | TYR53 |
A | TRP56 |
A | GLY159 |
A | CYS160 |
A | CYS163 |
A | HIS164 |
A | PHE171 |
A | GLY174 |
A | ARG201 |
A | GLN205 |
A | ILE283 |
A | MET287 |
A | LYS289 |
A | TYR298 |
A | THR299 |
A | HIS301 |
A | ILE303 |
A | HOH544 |
A | HOH634 |
A | HOH1049 |
site_id | AC5 |
Number of Residues | 28 |
Details | BINDING SITE FOR RESIDUE HEC A 5 |
Chain | Residue |
A | EU2 |
A | HEC3 |
A | HEC4 |
A | HEC6 |
A | GLN62 |
A | PRO91 |
A | ARG92 |
A | GLY93 |
A | HIS94 |
A | PHE96 |
A | ALA97 |
A | ASP100 |
A | CYS125 |
A | LYS126 |
A | LEU158 |
A | ARG182 |
A | VAL208 |
A | CYS209 |
A | CYS212 |
A | HIS213 |
A | ILE283 |
A | HIS286 |
A | MET287 |
A | ILE303 |
A | GLY304 |
A | HOH620 |
A | HOH626 |
A | HOH854 |
site_id | AC6 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE HEC A 6 |
Chain | Residue |
A | CYS282 |
A | CYS285 |
A | HIS286 |
A | PRO306 |
A | PHE307 |
A | HIS388 |
A | HIS391 |
A | MET392 |
A | HIS393 |
A | HOH596 |
A | HOH724 |
A | HOH825 |
A | HOH843 |
A | HOH854 |
A | HOH1189 |
A | EU2 |
A | HEC5 |
A | HEC7 |
A | PRO91 |
A | HIS213 |
A | GLU266 |
A | TRP270 |
A | HIS275 |
A | VAL280 |
A | THR281 |
site_id | AC7 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE HEC A 7 |
Chain | Residue |
A | HEC6 |
A | HIS275 |
A | VAL280 |
A | ASP284 |
A | PRO306 |
A | PHE307 |
A | THR313 |
A | CYS314 |
A | CYS317 |
A | HIS318 |
A | ARG332 |
A | MET392 |
A | EU479 |
A | EU480 |
A | HOH534 |
A | HOH897 |
D | HEC7 |
D | HIS318 |
D | GLN320 |
D | GLU396 |
site_id | AC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EU A 479 |
Chain | Residue |
A | HEC7 |
A | HOH1459 |
D | HEC7 |
D | HOH652 |
site_id | AC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EU A 480 |
Chain | Residue |
A | HEC7 |
A | GLU396 |
D | HEC7 |
D | GLU396 |
site_id | BC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA B 1 |
Chain | Residue |
B | GLU215 |
B | TYR216 |
B | LYS261 |
B | GLN263 |
B | HOH566 |
B | HOH635 |
site_id | BC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE EU B 2 |
Chain | Residue |
B | HEC5 |
B | HEC6 |
B | PRO91 |
B | HOH541 |
B | HOH562 |
B | HOH686 |
B | HOH690 |
B | HOH1976 |
site_id | BC3 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE HEC B 3 |
Chain | Residue |
B | HEC5 |
B | HOH11 |
B | HOH22 |
B | TYR88 |
B | ASN89 |
B | PRO91 |
B | ASP100 |
B | THR104 |
B | ARG106 |
B | THR107 |
B | CYS122 |
B | CYS125 |
B | LYS126 |
B | CYS212 |
B | HIS213 |
B | TYR216 |
B | PHE218 |
B | HIS264 |
B | HIS388 |
B | HOH495 |
B | HOH504 |
B | HOH509 |
B | HOH527 |
B | HOH533 |
B | HOH557 |
B | HOH829 |
site_id | BC4 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE HEC B 4 |
Chain | Residue |
B | HEC5 |
B | HIS49 |
B | GLN52 |
B | TYR53 |
B | TRP56 |
B | GLY159 |
B | CYS160 |
B | CYS163 |
B | HIS164 |
B | PHE171 |
B | GLY174 |
B | ARG201 |
B | GLN205 |
B | ILE283 |
B | MET287 |
B | LYS289 |
B | TYR298 |
B | THR299 |
B | HIS301 |
B | HOH529 |
B | HOH570 |
B | HOH1105 |
site_id | BC5 |
Number of Residues | 29 |
Details | BINDING SITE FOR RESIDUE HEC B 5 |
Chain | Residue |
B | EU2 |
B | HEC3 |
B | HEC4 |
B | HEC6 |
B | GLN62 |
B | PRO91 |
B | ARG92 |
B | GLY93 |
B | HIS94 |
B | PHE96 |
B | ALA97 |
B | ASP100 |
B | CYS125 |
B | LYS126 |
B | LEU158 |
B | ARG182 |
B | VAL208 |
B | CYS209 |
B | CYS212 |
B | HIS213 |
B | ILE283 |
B | HIS286 |
B | MET287 |
B | ILE303 |
B | GLY304 |
B | HOH562 |
B | HOH567 |
B | HOH690 |
B | HOH1350 |
site_id | BC6 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE HEC B 6 |
Chain | Residue |
B | EU2 |
B | HEC5 |
B | HEC7 |
B | PRO91 |
B | HIS213 |
B | GLU266 |
B | TRP270 |
B | HIS275 |
B | VAL280 |
B | THR281 |
B | CYS282 |
B | CYS285 |
B | HIS286 |
B | ASN305 |
B | PRO306 |
B | PHE307 |
B | HIS388 |
B | HIS391 |
B | MET392 |
B | HIS393 |
B | HOH492 |
B | HOH686 |
B | HOH687 |
B | HOH690 |
B | HOH823 |
B | HOH1433 |
site_id | BC7 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC B 7 |
Chain | Residue |
B | HEC6 |
B | ILE274 |
B | HIS275 |
B | VAL280 |
B | ASP284 |
B | PRO306 |
B | PHE307 |
B | THR313 |
B | CYS314 |
B | CYS317 |
B | HIS318 |
B | ARG332 |
B | MET392 |
B | EU479 |
B | EU480 |
B | HOH644 |
B | HOH992 |
C | HEC7 |
C | HIS318 |
C | GLN320 |
C | GLU396 |
site_id | BC8 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EU B 479 |
Chain | Residue |
B | HEC7 |
B | HOH1718 |
C | HEC7 |
C | HOH611 |
site_id | BC9 |
Number of Residues | 4 |
Details | BINDING SITE FOR RESIDUE EU B 480 |
Chain | Residue |
B | HEC7 |
B | GLU396 |
C | HEC7 |
C | GLU396 |
site_id | CC1 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA C 1 |
Chain | Residue |
C | GLU215 |
C | TYR216 |
C | LYS261 |
C | GLN263 |
C | HOH509 |
C | HOH583 |
site_id | CC2 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE EU C 2 |
Chain | Residue |
C | HEC5 |
C | HEC6 |
C | PRO91 |
C | HOH645 |
C | HOH858 |
C | HOH1356 |
C | HOH1509 |
C | HOH1793 |
site_id | CC3 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE HEC C 3 |
Chain | Residue |
C | HEC5 |
C | TYR88 |
C | ASN89 |
C | PRO91 |
C | ASP100 |
C | THR104 |
C | ARG106 |
C | THR107 |
C | LEU118 |
C | CYS122 |
C | CYS125 |
C | LYS126 |
C | CYS212 |
C | HIS213 |
C | TYR216 |
C | HIS264 |
C | HIS388 |
C | HOH486 |
C | HOH488 |
C | HOH500 |
C | HOH505 |
C | HOH514 |
C | HOH515 |
C | HOH537 |
C | HOH634 |
C | HOH1045 |
site_id | CC4 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC C 4 |
Chain | Residue |
C | HEC5 |
C | HIS49 |
C | GLN52 |
C | TRP56 |
C | GLY159 |
C | CYS160 |
C | CYS163 |
C | HIS164 |
C | PHE171 |
C | GLY174 |
C | PRO176 |
C | LEU178 |
C | ARG201 |
C | GLN205 |
C | ILE283 |
C | LYS289 |
C | TYR298 |
C | THR299 |
C | HIS301 |
C | HOH539 |
C | HOH1720 |
site_id | CC5 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC C 5 |
Chain | Residue |
C | EU2 |
C | HEC3 |
C | HEC4 |
C | HEC6 |
C | GLN62 |
C | PRO91 |
C | ARG92 |
C | GLY93 |
C | HIS94 |
C | PHE96 |
C | ALA97 |
C | ASP100 |
C | CYS125 |
C | LYS126 |
C | LEU158 |
C | VAL208 |
C | CYS209 |
C | CYS212 |
C | HIS213 |
C | ILE283 |
C | HIS286 |
C | MET287 |
C | ILE303 |
C | HOH1509 |
site_id | CC6 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE HEC C 6 |
Chain | Residue |
C | EU2 |
C | HEC5 |
C | HEC7 |
C | PRO91 |
C | HIS213 |
C | GLU266 |
C | TRP270 |
C | HIS275 |
C | VAL280 |
C | THR281 |
C | CYS282 |
C | CYS285 |
C | HIS286 |
C | ASN305 |
C | PRO306 |
C | PHE307 |
C | HIS388 |
C | GLY389 |
C | HIS391 |
C | MET392 |
C | HIS393 |
C | HOH693 |
C | HOH835 |
C | HOH1183 |
C | HOH1356 |
site_id | CC7 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC C 7 |
Chain | Residue |
B | HEC7 |
B | ILE274 |
B | HIS318 |
B | GLN320 |
B | GLU396 |
B | EU479 |
B | EU480 |
C | HEC6 |
C | ILE274 |
C | HIS275 |
C | VAL280 |
C | ASP284 |
C | PHE307 |
C | THR313 |
C | CYS314 |
C | CYS317 |
C | HIS318 |
C | ARG332 |
C | MET392 |
C | HOH961 |
C | HOH969 |
site_id | CC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EU C 479 |
Chain | Residue |
A | ASP457 |
A | HOH826 |
A | HOH1514 |
C | GLU190 |
C | HOH521 |
C | HOH622 |
C | HOH866 |
site_id | CC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA D 1 |
Chain | Residue |
D | GLU215 |
D | TYR216 |
D | LYS261 |
D | GLN263 |
D | HOH509 |
D | HOH543 |
site_id | DC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE EU D 2 |
Chain | Residue |
D | HEC5 |
D | HEC6 |
D | PRO91 |
D | HOH725 |
D | HOH783 |
D | HOH1000 |
D | HOH1042 |
site_id | DC2 |
Number of Residues | 28 |
Details | BINDING SITE FOR RESIDUE HEC D 3 |
Chain | Residue |
D | HEC5 |
D | HOH17 |
D | TYR88 |
D | ASN89 |
D | PRO91 |
D | ASP100 |
D | THR104 |
D | ARG106 |
D | THR107 |
D | LEU118 |
D | CYS122 |
D | CYS125 |
D | LYS126 |
D | CYS212 |
D | HIS213 |
D | TYR216 |
D | PHE218 |
D | VAL225 |
D | HIS264 |
D | HIS388 |
D | HOH485 |
D | HOH489 |
D | HOH496 |
D | HOH517 |
D | HOH542 |
D | HOH590 |
D | HOH613 |
D | HOH818 |
site_id | DC3 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE HEC D 4 |
Chain | Residue |
D | HEC5 |
D | HIS49 |
D | GLN52 |
D | TYR53 |
D | TRP56 |
D | GLY159 |
D | CYS160 |
D | CYS163 |
D | HIS164 |
D | PHE171 |
D | GLY174 |
D | PRO176 |
D | ARG201 |
D | GLN205 |
D | ILE283 |
D | LYS289 |
D | TYR298 |
D | THR299 |
D | HIS301 |
D | HOH515 |
D | HOH1968 |
site_id | DC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE HEC D 5 |
Chain | Residue |
D | EU2 |
D | HEC3 |
D | HEC4 |
D | HEC6 |
D | GLN62 |
D | PRO91 |
D | ARG92 |
D | GLY93 |
D | HIS94 |
D | PHE96 |
D | ALA97 |
D | ASP100 |
D | CYS125 |
D | LEU158 |
D | VAL208 |
D | CYS209 |
D | CYS212 |
D | HIS213 |
D | ILE283 |
D | HIS286 |
D | MET287 |
D | ILE303 |
D | HOH522 |
D | HOH1042 |
site_id | DC5 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE HEC D 6 |
Chain | Residue |
D | EU2 |
D | HEC5 |
D | HEC7 |
D | PRO91 |
D | HIS213 |
D | GLU266 |
D | TRP270 |
D | HIS275 |
D | VAL280 |
D | THR281 |
D | CYS282 |
D | CYS285 |
D | HIS286 |
D | ASN305 |
D | PRO306 |
D | HIS388 |
D | HIS391 |
D | MET392 |
D | HIS393 |
D | HOH725 |
D | HOH844 |
D | HOH1065 |
site_id | DC6 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE HEC D 7 |
Chain | Residue |
A | HEC7 |
A | ILE274 |
A | HIS318 |
A | GLN320 |
A | GLU396 |
A | EU479 |
A | EU480 |
D | HEC6 |
D | HIS275 |
D | VAL280 |
D | PHE307 |
D | THR313 |
D | CYS314 |
D | CYS317 |
D | HIS318 |
D | ARG332 |
D | MET392 |
D | HOH591 |
D | HOH1060 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 36 |
Details | BINDING: axial binding residue => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR |
Chain | Residue | Details |
A | HIS393 | |
B | HIS94 | |
B | LYS126 | |
B | HIS164 | |
B | HIS213 | |
B | HIS275 | |
B | HIS286 | |
B | HIS301 | |
B | HIS318 | |
B | HIS393 | |
C | HIS94 | |
C | LYS126 | |
C | HIS164 | |
C | HIS213 | |
C | HIS275 | |
C | HIS286 | |
C | HIS301 | |
C | HIS318 | |
C | HIS393 | |
D | HIS94 | |
D | LYS126 | |
D | HIS164 | |
D | HIS213 | |
D | HIS275 | |
D | HIS286 | |
D | HIS301 | |
D | HIS318 | |
D | HIS393 | |
A | HIS94 | |
A | LYS126 | |
A | HIS164 | |
A | HIS213 | |
A | HIS275 | |
A | HIS286 | |
A | HIS301 | |
A | HIS318 |
site_id | SWS_FT_FI2 |
Number of Residues | 32 |
Details | BINDING: covalent => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR |
Chain | Residue | Details |
A | CYS209 | |
A | CYS212 | |
A | CYS282 | |
A | CYS314 | |
B | CYS122 | |
B | CYS125 | |
B | CYS160 | |
B | CYS163 | |
B | CYS209 | |
B | CYS212 | |
B | CYS282 | |
B | CYS314 | |
C | CYS122 | |
C | CYS125 | |
C | CYS160 | |
C | CYS163 | |
C | CYS209 | |
C | CYS212 | |
C | CYS282 | |
C | CYS314 | |
D | CYS122 | |
D | CYS125 | |
D | CYS160 | |
D | CYS163 | |
D | CYS209 | |
D | CYS212 | |
D | CYS282 | |
D | CYS314 | |
A | CYS122 | |
A | CYS125 | |
A | CYS160 | |
A | CYS163 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR |
Chain | Residue | Details |
A | GLU215 | |
A | LYS261 | |
B | GLU215 | |
B | LYS261 | |
C | GLU215 | |
C | LYS261 | |
D | GLU215 | |
D | LYS261 |
site_id | SWS_FT_FI4 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000305 |
Chain | Residue | Details |
C | TYR216 | |
C | HIS264 | |
D | TYR216 | |
D | HIS264 | |
A | HIS264 | |
B | TYR216 | |
B | HIS264 | |
A | TYR216 |
site_id | SWS_FT_FI5 |
Number of Residues | 4 |
Details | BINDING: BINDING => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR |
Chain | Residue | Details |
A | GLN263 | |
B | GLN263 | |
C | GLN263 | |
D | GLN263 |
site_id | SWS_FT_FI6 |
Number of Residues | 8 |
Details | BINDING: covalent => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7 |
Chain | Residue | Details |
C | CYS285 | |
C | CYS317 | |
D | CYS285 | |
D | CYS317 | |
A | CYS285 | |
A | CYS317 | |
B | CYS285 | |
B | CYS317 |