6Z8J
Structure of [NiFeSe] hydrogenase from Desulfovibrio vulgaris hildenborough pressurized with Oxygen gas - structure wtO2
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 | 0005515 | molecular_function | protein binding |
| B | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| B | 0016151 | molecular_function | nickel cation binding |
| B | 0016491 | molecular_function | oxidoreductase activity |
| B | 0042597 | cellular_component | periplasmic space |
| B | 0046872 | molecular_function | metal ion binding |
| B | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| C | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| C | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| C | 0051536 | molecular_function | iron-sulfur cluster binding |
| D | 0005515 | molecular_function | protein binding |
| D | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| D | 0016151 | molecular_function | nickel cation binding |
| D | 0016491 | molecular_function | oxidoreductase activity |
| D | 0042597 | cellular_component | periplasmic space |
| D | 0046872 | molecular_function | metal ion binding |
| D | 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 301 |
| Chain | Residue |
| A | HIS208 |
| A | CYS211 |
| A | TYR213 |
| A | LEU214 |
| A | CYS232 |
| A | ARG233 |
| A | CYS238 |
| A | VAL260 |
| site_id | AC2 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 A 302 |
| Chain | Residue |
| A | CYS247 |
| A | TRP252 |
| A | CYS259 |
| A | CYS265 |
| A | ILE266 |
| A | CYS268 |
| B | ARG182 |
| B | GLN187 |
| A | THR243 |
| site_id | AC3 |
| Number of Residues | 12 |
| Details | binding site for residue SF4 A 303 |
| Chain | Residue |
| A | GLY17 |
| A | CYS18 |
| A | CYS21 |
| A | GLY119 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| A | PRO160 |
| A | 6ML304 |
| B | ARG73 |
| B | HIS185 |
| site_id | AC4 |
| Number of Residues | 14 |
| Details | binding site for residue 6ML A 304 |
| Chain | Residue |
| A | CYS18 |
| A | THR19 |
| A | GLY20 |
| A | CYS21 |
| A | GLU77 |
| A | GLY78 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| A | PRO160 |
| A | SF4303 |
| A | HOH411 |
| B | HIS185 |
| site_id | AC5 |
| Number of Residues | 8 |
| Details | binding site for residue GOL A 305 |
| Chain | Residue |
| A | ASP85 |
| A | GLY86 |
| A | LYS87 |
| A | HIS97 |
| A | GLU98 |
| A | SER100 |
| A | ASP103 |
| A | HOH449 |
| site_id | AC6 |
| Number of Residues | 11 |
| Details | binding site for residue FCO B 501 |
| Chain | Residue |
| B | CYS78 |
| B | ALA420 |
| B | PRO421 |
| B | ARG422 |
| B | LEU425 |
| B | ALA444 |
| B | SER445 |
| B | SEC489 |
| B | CYS492 |
| B | NI502 |
| B | H2S504 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue NI B 502 |
| Chain | Residue |
| B | CSD75 |
| B | CYS78 |
| B | SEC489 |
| B | CYS492 |
| B | FCO501 |
| B | H2S504 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 B 503 |
| Chain | Residue |
| B | GLU56 |
| B | ILE441 |
| B | HIS495 |
| B | HOH622 |
| B | HOH625 |
| B | HOH633 |
| site_id | AC9 |
| Number of Residues | 6 |
| Details | binding site for residue CL B 505 |
| Chain | Residue |
| B | CYS78 |
| B | THR80 |
| B | ALA81 |
| B | PHE110 |
| B | ASN113 |
| B | PRO421 |
| site_id | AD1 |
| Number of Residues | 7 |
| Details | binding site for residue GOL B 506 |
| Chain | Residue |
| A | MET222 |
| A | ASP228 |
| A | VAL230 |
| B | GLY15 |
| B | ASN39 |
| B | HOH673 |
| B | HOH765 |
| site_id | AD2 |
| Number of Residues | 4 |
| Details | binding site for residue GOL B 507 |
| Chain | Residue |
| B | VAL248 |
| B | PRO264 |
| B | PHE275 |
| B | PRO277 |
| site_id | AD3 |
| Number of Residues | 2 |
| Details | binding site for residue OXY B 508 |
| Chain | Residue |
| B | GLY133 |
| B | TYR162 |
| site_id | AD4 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 C 301 |
| Chain | Residue |
| C | CYS238 |
| C | VAL260 |
| C | HIS208 |
| C | CYS211 |
| C | TYR213 |
| C | LEU214 |
| C | CYS232 |
| C | ARG233 |
| site_id | AD5 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 C 302 |
| Chain | Residue |
| C | THR243 |
| C | CYS247 |
| C | TRP252 |
| C | CYS259 |
| C | CYS265 |
| C | ILE266 |
| C | CYS268 |
| D | ARG182 |
| D | GLN187 |
| site_id | AD6 |
| Number of Residues | 12 |
| Details | binding site for residue SF4 C 303 |
| Chain | Residue |
| C | GLY17 |
| C | CYS18 |
| C | CYS21 |
| C | GLY119 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | PRO160 |
| C | 6ML304 |
| D | ARG73 |
| D | HIS185 |
| site_id | AD7 |
| Number of Residues | 14 |
| Details | binding site for residue 6ML C 304 |
| Chain | Residue |
| C | CYS18 |
| C | THR19 |
| C | GLY20 |
| C | CYS21 |
| C | GLU77 |
| C | GLY78 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | PRO160 |
| C | SF4303 |
| C | HOH411 |
| D | HIS185 |
| site_id | AD8 |
| Number of Residues | 8 |
| Details | binding site for residue GOL C 305 |
| Chain | Residue |
| C | ASP85 |
| C | GLY86 |
| C | LYS87 |
| C | ILE90 |
| C | GLU98 |
| C | SER100 |
| C | HOH444 |
| C | HOH566 |
| site_id | AD9 |
| Number of Residues | 11 |
| Details | binding site for residue FCO D 501 |
| Chain | Residue |
| D | CYS78 |
| D | ALA420 |
| D | PRO421 |
| D | ARG422 |
| D | LEU425 |
| D | ALA444 |
| D | SER445 |
| D | SEC489 |
| D | CYS492 |
| D | NI502 |
| D | H2S504 |
| site_id | AE1 |
| Number of Residues | 6 |
| Details | binding site for residue NI D 502 |
| Chain | Residue |
| D | CSD75 |
| D | CYS78 |
| D | SEC489 |
| D | CYS492 |
| D | FCO501 |
| D | H2S504 |
| site_id | AE2 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 D 503 |
| Chain | Residue |
| D | GLU56 |
| D | ILE441 |
| D | HIS495 |
| D | HOH614 |
| D | HOH617 |
| D | HOH618 |
| site_id | AE3 |
| Number of Residues | 6 |
| Details | binding site for residue CL D 505 |
| Chain | Residue |
| D | CYS78 |
| D | THR80 |
| D | ALA81 |
| D | PHE110 |
| D | ASN113 |
| D | PRO421 |
| site_id | AE4 |
| Number of Residues | 3 |
| Details | binding site for residue OXY D 506 |
| Chain | Residue |
| D | VAL131 |
| D | PHE139 |
| D | TYR162 |
| site_id | AE5 |
| Number of Residues | 13 |
| Details | binding site for residues H2S B 504 and SEC B 489 |
| Chain | Residue |
| B | GLU28 |
| B | CSD75 |
| B | CYS78 |
| B | ARG422 |
| B | SER445 |
| B | ASP487 |
| B | PRO488 |
| B | LEU490 |
| B | GLY491 |
| B | CYS492 |
| B | ALA493 |
| B | FCO501 |
| B | NI502 |
| site_id | AE6 |
| Number of Residues | 13 |
| Details | binding site for residues H2S D 504 and SEC D 489 |
| Chain | Residue |
| D | GLU28 |
| D | CSD75 |
| D | CYS78 |
| D | ARG422 |
| D | SER445 |
| D | ASP487 |
| D | PRO488 |
| D | LEU490 |
| D | GLY491 |
| D | CYS492 |
| D | ALA493 |
| D | FCO501 |
| D | NI502 |
Functional Information from PROSITE/UniProt
| site_id | PS00507 |
| Number of Residues | 26 |
| Details | NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGFEtilrgrdprdasqivQRiCGVC |
| Chain | Residue | Details |
| B | ARG53-CYS78 |
| site_id | PS00508 |
| Number of Residues | 10 |
| Details | NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPULGCav.H |
| Chain | Residue | Details |
| B | PHE486-HIS495 |
