4UD6
Structure of methylviologen-treated anaerobically purified D. fructosovorans NiFe-hydrogenase
Functional Information from GO Data
| Chain | GOid | namespace | contents |
| A | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| A | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| A | 0051536 | molecular_function | iron-sulfur cluster binding |
| B | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| B | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| B | 0051536 | molecular_function | iron-sulfur cluster binding |
| C | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| C | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| C | 0051536 | molecular_function | iron-sulfur cluster binding |
| Q | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| Q | 0016151 | molecular_function | nickel cation binding |
| Q | 0016491 | molecular_function | oxidoreductase activity |
| Q | 0042597 | cellular_component | periplasmic space |
| Q | 0046872 | molecular_function | metal ion binding |
| Q | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| R | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| R | 0016151 | molecular_function | nickel cation binding |
| R | 0016491 | molecular_function | oxidoreductase activity |
| R | 0042597 | cellular_component | periplasmic space |
| R | 0046872 | molecular_function | metal ion binding |
| R | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| S | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| S | 0016151 | molecular_function | nickel cation binding |
| S | 0016491 | molecular_function | oxidoreductase activity |
| S | 0042597 | cellular_component | periplasmic space |
| S | 0046872 | molecular_function | metal ion binding |
| S | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 A 1265 |
| Chain | Residue |
| A | HIS184 |
| A | CYS187 |
| A | ARG189 |
| A | LEU190 |
| A | CYS212 |
| A | LEU213 |
| A | CYS218 |
| A | PRO221 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S A 1266 |
| Chain | Residue |
| A | CYS227 |
| A | PHE232 |
| A | TRP237 |
| A | CYS245 |
| A | LEU246 |
| A | CYS248 |
| Q | LYS225 |
| Q | GLN230 |
| A | ASN225 |
| site_id | AC3 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 A 1267 |
| Chain | Residue |
| A | GLU16 |
| A | CYS17 |
| A | CYS20 |
| A | GLY112 |
| A | THR113 |
| A | CYS114 |
| A | GLY146 |
| A | CYS147 |
| Q | ARG70 |
| Q | HIS228 |
| site_id | AC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 1271 |
| Chain | Residue |
| A | ASP168 |
| A | LEU169 |
| A | LYS176 |
| A | GOL1272 |
| A | HOH2213 |
| A | HOH2323 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL A 1272 |
| Chain | Residue |
| A | LYS140 |
| A | LEU169 |
| A | ASP170 |
| A | GOL1271 |
| A | HOH2324 |
| site_id | AC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL A 1273 |
| Chain | Residue |
| A | ARG6 |
| A | LEU37 |
| A | ASP38 |
| A | HOH2325 |
| Q | ALA169 |
| Q | PHE170 |
| site_id | AC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 B 1265 |
| Chain | Residue |
| B | HIS184 |
| B | CYS187 |
| B | ARG189 |
| B | LEU190 |
| B | PHE193 |
| B | CYS212 |
| B | LEU213 |
| B | CYS218 |
| site_id | AC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE F3S B 1266 |
| Chain | Residue |
| B | ASN225 |
| B | CYS227 |
| B | PHE232 |
| B | CYS245 |
| B | LEU246 |
| B | CYS248 |
| R | LYS225 |
| R | GLN230 |
| site_id | AC9 |
| Number of Residues | 11 |
| Details | BINDING SITE FOR RESIDUE SF4 B 1267 |
| Chain | Residue |
| B | GLU16 |
| B | CYS17 |
| B | CYS20 |
| B | GLY112 |
| B | THR113 |
| B | CYS114 |
| B | GLY146 |
| B | CYS147 |
| B | PRO148 |
| R | ARG70 |
| R | HIS228 |
| site_id | BC1 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 C 1265 |
| Chain | Residue |
| C | HIS184 |
| C | CYS187 |
| C | ARG189 |
| C | LEU190 |
| C | CYS212 |
| C | LEU213 |
| C | CYS218 |
| C | PRO221 |
| site_id | BC2 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE F3S C 1266 |
| Chain | Residue |
| C | ASN225 |
| C | CYS227 |
| C | PHE232 |
| C | TRP237 |
| C | CYS245 |
| C | LEU246 |
| C | CYS248 |
| S | LYS225 |
| S | GLN230 |
| site_id | BC3 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE SF4 C 1267 |
| Chain | Residue |
| C | CYS17 |
| C | CYS20 |
| C | THR113 |
| C | CYS114 |
| C | GLY146 |
| C | CYS147 |
| C | PRO148 |
| S | ARG70 |
| S | HIS228 |
| site_id | BC4 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO Q 1550 |
| Chain | Residue |
| Q | HIS79 |
| Q | ALA474 |
| Q | PRO475 |
| Q | ARG476 |
| Q | LEU479 |
| Q | VAL497 |
| Q | PRO498 |
| Q | SER499 |
| Q | CSO543 |
| Q | CYS546 |
| Q | NI1551 |
| Q | CYS75 |
| Q | VAL78 |
| site_id | BC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI Q 1551 |
| Chain | Residue |
| Q | CYS72 |
| Q | CYS75 |
| Q | CSO543 |
| Q | CYS546 |
| Q | FCO1550 |
| site_id | BC6 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG Q 1553 |
| Chain | Residue |
| Q | GLU53 |
| Q | LEU495 |
| Q | HIS549 |
| Q | HOH2051 |
| Q | HOH2052 |
| Q | HOH2312 |
| site_id | BC7 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL Q 1561 |
| Chain | Residue |
| Q | ARG100 |
| Q | ASN104 |
| Q | PHE295 |
| Q | ALA296 |
| Q | THR297 |
| Q | GLU445 |
| Q | HOH2112 |
| Q | HOH2442 |
| site_id | BC8 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL Q 1562 |
| Chain | Residue |
| A | ALA55 |
| C | PHE198 |
| C | HOH2176 |
| C | HOH2200 |
| Q | ASN181 |
| Q | ALA182 |
| Q | LEU185 |
| Q | ARG529 |
| site_id | BC9 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL Q 1563 |
| Chain | Residue |
| Q | GLY281 |
| Q | GLY282 |
| Q | ILE283 |
| Q | GLY284 |
| Q | GLY285 |
| Q | ARG319 |
| Q | HIS419 |
| Q | HOH2370 |
| Q | HOH2443 |
| site_id | CC1 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE GOL Q 1564 |
| Chain | Residue |
| Q | LYS245 |
| Q | LYS337 |
| Q | TYR338 |
| Q | ASP366 |
| Q | HOH2444 |
| site_id | CC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL R 1001 |
| Chain | Residue |
| R | GLY281 |
| R | GLY282 |
| R | ILE283 |
| R | GLY284 |
| R | GLY285 |
| R | ARG319 |
| R | HIS419 |
| R | HOH2259 |
| site_id | CC3 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE GOL R 1002 |
| Chain | Residue |
| R | THR286 |
| R | SER287 |
| R | ASN288 |
| R | ALA380 |
| R | PRO514 |
| R | GLU517 |
| R | HOH2225 |
| R | HOH2380 |
| site_id | CC4 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE GOL R 1003 |
| Chain | Residue |
| R | ARG152 |
| R | PRO153 |
| R | SER156 |
| R | HOH2130 |
| R | HOH2137 |
| S | ALA451 |
| site_id | CC5 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL R 1004 |
| Chain | Residue |
| C | ALA103 |
| R | GLU465 |
| R | SER466 |
| R | LYS467 |
| R | ARG484 |
| R | HOH2366 |
| R | HOH2367 |
| site_id | CC6 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO R 1550 |
| Chain | Residue |
| R | CYS75 |
| R | VAL78 |
| R | HIS79 |
| R | ALA474 |
| R | PRO475 |
| R | ARG476 |
| R | LEU479 |
| R | VAL497 |
| R | PRO498 |
| R | SER499 |
| R | CSO543 |
| R | CYS546 |
| R | NI1551 |
| site_id | CC7 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI R 1551 |
| Chain | Residue |
| R | CYS72 |
| R | CYS75 |
| R | CSO543 |
| R | CYS546 |
| R | FCO1550 |
| site_id | CC8 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG R 1553 |
| Chain | Residue |
| R | GLU53 |
| R | LEU495 |
| R | HIS549 |
| R | HOH2049 |
| R | HOH2050 |
| R | HOH2275 |
| site_id | CC9 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL R 1561 |
| Chain | Residue |
| B | ALA55 |
| R | ASN181 |
| R | ALA182 |
| R | TYR183 |
| R | LEU185 |
| R | ARG529 |
| R | HOH2389 |
| site_id | DC1 |
| Number of Residues | 4 |
| Details | BINDING SITE FOR RESIDUE GOL R 1562 |
| Chain | Residue |
| B | LEU137 |
| R | GLY409 |
| R | LYS410 |
| R | HOH2336 |
| site_id | DC2 |
| Number of Residues | 10 |
| Details | BINDING SITE FOR RESIDUE GOL R 1563 |
| Chain | Residue |
| R | ARG100 |
| R | ASN104 |
| R | PHE295 |
| R | ALA296 |
| R | THR297 |
| R | GLN310 |
| R | GLU445 |
| R | HOH2098 |
| R | HOH2101 |
| R | HOH2245 |
| site_id | DC3 |
| Number of Residues | 13 |
| Details | BINDING SITE FOR RESIDUE FCO S 1550 |
| Chain | Residue |
| S | CYS75 |
| S | VAL78 |
| S | HIS79 |
| S | ALA474 |
| S | PRO475 |
| S | ARG476 |
| S | LEU479 |
| S | VAL497 |
| S | PRO498 |
| S | SER499 |
| S | CSO543 |
| S | CYS546 |
| S | NI1551 |
| site_id | DC4 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE NI S 1551 |
| Chain | Residue |
| S | CYS72 |
| S | CYS75 |
| S | CSO543 |
| S | CYS546 |
| S | FCO1550 |
| site_id | DC5 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE MG S 1553 |
| Chain | Residue |
| S | GLU53 |
| S | LEU495 |
| S | HIS549 |
| S | HOH2023 |
| S | HOH2024 |
| S | HOH2196 |
| site_id | DC6 |
| Number of Residues | 9 |
| Details | BINDING SITE FOR RESIDUE GOL S 1561 |
| Chain | Residue |
| S | ARG100 |
| S | ASN104 |
| S | PHE295 |
| S | ALA296 |
| S | THR297 |
| S | GLU445 |
| S | HOH2074 |
| S | HOH2183 |
| S | HOH2279 |
Functional Information from PROSITE/UniProt
| site_id | PS00507 |
| Number of Residues | 26 |
| Details | NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEiilkgrdprdaqhftQRaCGVC |
| Chain | Residue | Details |
| Q | ARG50-CYS75 |
| site_id | PS00508 |
| Number of Residues | 10 |
| Details | NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPCIACgv.H |
| Chain | Residue | Details |
| Q | PHE540-HIS549 |
