6Z9G
Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Oxygen gas - structure G491A-O2
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 |
| E | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| E | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| E | 0051536 | molecular_function | iron-sulfur cluster binding |
| F | 0005515 | molecular_function | protein binding |
| F | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| F | 0016151 | molecular_function | nickel cation binding |
| F | 0016491 | molecular_function | oxidoreductase activity |
| F | 0042597 | cellular_component | periplasmic space |
| F | 0046872 | molecular_function | metal ion binding |
| F | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
| G | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| G | 0009375 | cellular_component | ferredoxin hydrogenase complex |
| G | 0051536 | molecular_function | iron-sulfur cluster binding |
| H | 0005515 | molecular_function | protein binding |
| H | 0008901 | molecular_function | ferredoxin hydrogenase activity |
| H | 0016151 | molecular_function | nickel cation binding |
| H | 0016491 | molecular_function | oxidoreductase activity |
| H | 0042597 | cellular_component | periplasmic space |
| H | 0046872 | molecular_function | metal ion binding |
| H | 0047806 | molecular_function | cytochrome-c3 hydrogenase activity |
Functional Information from PDB Data
| site_id | AC1 |
| Number of Residues | 10 |
| Details | binding site for residue SF4 A 301 |
| Chain | Residue |
| A | HIS208 |
| A | VAL260 |
| A | CYS211 |
| A | TYR213 |
| A | LEU214 |
| A | TYR217 |
| A | CYS232 |
| A | ARG233 |
| A | TYR234 |
| A | CYS238 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 A 302 |
| Chain | Residue |
| A | THR243 |
| A | CYS247 |
| A | TRP252 |
| A | CYS259 |
| A | CYS265 |
| A | ILE266 |
| A | CYS268 |
| B | ARG182 |
| site_id | AC3 |
| Number of Residues | 11 |
| Details | binding site for residue SF4 A 303 |
| Chain | Residue |
| A | CYS18 |
| A | CYS21 |
| A | GLU77 |
| A | GLY119 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| 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 | GLY119 |
| A | THR120 |
| A | CYS121 |
| A | GLY158 |
| A | CYS159 |
| A | SF4303 |
| B | ARG73 |
| B | HIS185 |
| site_id | AC5 |
| Number of Residues | 10 |
| Details | binding site for residue FCO B 500 |
| Chain | Residue |
| B | CYS78 |
| B | ALA420 |
| B | PRO421 |
| B | ARG422 |
| B | ALA444 |
| B | SER445 |
| B | SEC489 |
| B | CYS492 |
| B | NI501 |
| B | H2S503 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | binding site for residue NI B 501 |
| Chain | Residue |
| B | CYS75 |
| B | CSD75 |
| B | CYS78 |
| B | SEC489 |
| B | CYS492 |
| B | FCO500 |
| B | H2S503 |
| site_id | AC7 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 B 502 |
| Chain | Residue |
| B | GLU56 |
| B | ILE441 |
| B | HIS495 |
| B | HOH602 |
| B | HOH613 |
| B | HOH711 |
| site_id | AC8 |
| Number of Residues | 6 |
| Details | binding site for residue CL B 504 |
| Chain | Residue |
| B | CYS78 |
| B | THR80 |
| B | ALA81 |
| B | PHE110 |
| B | ASN113 |
| B | PRO421 |
| site_id | AC9 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 C 301 |
| Chain | Residue |
| C | HIS208 |
| C | CYS211 |
| C | TYR213 |
| C | LEU214 |
| C | CYS232 |
| C | ARG233 |
| C | CYS238 |
| C | VAL260 |
| site_id | AD1 |
| Number of Residues | 8 |
| 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 |
| site_id | AD2 |
| Number of Residues | 12 |
| Details | binding site for residue SF4 C 303 |
| Chain | Residue |
| D | HIS185 |
| C | CYS18 |
| C | CYS21 |
| C | GLU77 |
| C | GLY119 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | PRO160 |
| C | 6ML304 |
| D | ARG73 |
| site_id | AD3 |
| Number of Residues | 17 |
| Details | binding site for residue 6ML C 304 |
| Chain | Residue |
| C | CYS18 |
| C | THR19 |
| C | GLY20 |
| C | CYS21 |
| C | GLU77 |
| C | GLY78 |
| C | GLY119 |
| C | THR120 |
| C | CYS121 |
| C | GLY158 |
| C | CYS159 |
| C | PRO160 |
| C | PRO161 |
| C | SF4303 |
| C | HOH415 |
| D | ARG73 |
| D | HIS185 |
| site_id | AD4 |
| Number of Residues | 11 |
| Details | binding site for residue FCO D 500 |
| Chain | Residue |
| D | CYS78 |
| D | HIS82 |
| D | ALA420 |
| D | PRO421 |
| D | ARG422 |
| D | ALA444 |
| D | SER445 |
| D | SEC489 |
| D | CYS492 |
| D | NI501 |
| D | H2S503 |
| site_id | AD5 |
| Number of Residues | 7 |
| Details | binding site for residue NI D 501 |
| Chain | Residue |
| D | CYS75 |
| D | CSD75 |
| D | CYS78 |
| D | SEC489 |
| D | CYS492 |
| D | FCO500 |
| D | H2S503 |
| site_id | AD6 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 D 502 |
| Chain | Residue |
| D | GLU56 |
| D | ILE441 |
| D | HIS495 |
| D | HOH603 |
| D | HOH606 |
| D | HOH608 |
| site_id | AD7 |
| Number of Residues | 6 |
| Details | binding site for residue CL D 504 |
| Chain | Residue |
| D | CYS78 |
| D | THR80 |
| D | ALA81 |
| D | PHE110 |
| D | ASN113 |
| D | PRO421 |
| site_id | AD8 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 E 301 |
| Chain | Residue |
| E | HIS208 |
| E | CYS211 |
| E | TYR213 |
| E | LEU214 |
| E | CYS232 |
| E | ARG233 |
| E | CYS238 |
| E | VAL260 |
| site_id | AD9 |
| Number of Residues | 9 |
| Details | binding site for residue SF4 E 302 |
| Chain | Residue |
| E | THR243 |
| E | CYS247 |
| E | TRP252 |
| E | CYS259 |
| E | CYS265 |
| E | ILE266 |
| E | CYS268 |
| F | ARG182 |
| F | GLN187 |
| site_id | AE1 |
| Number of Residues | 13 |
| Details | binding site for residue SF4 E 303 |
| Chain | Residue |
| E | GLY17 |
| E | CYS18 |
| E | CYS21 |
| E | GLU77 |
| E | GLY119 |
| E | THR120 |
| E | CYS121 |
| E | GLY158 |
| E | CYS159 |
| E | PRO160 |
| E | 6ML304 |
| F | ARG73 |
| F | HIS185 |
| site_id | AE2 |
| Number of Residues | 15 |
| Details | binding site for residue 6ML E 304 |
| Chain | Residue |
| E | CYS18 |
| E | THR19 |
| E | GLY20 |
| E | CYS21 |
| E | GLU77 |
| E | GLY78 |
| E | THR120 |
| E | CYS121 |
| E | GLY158 |
| E | CYS159 |
| E | PRO160 |
| E | SF4303 |
| E | HOH418 |
| F | ARG73 |
| F | HIS185 |
| site_id | AE3 |
| Number of Residues | 12 |
| Details | binding site for residue FCO F 500 |
| Chain | Residue |
| F | CYS78 |
| F | HIS82 |
| F | ALA420 |
| F | PRO421 |
| F | ARG422 |
| F | LEU425 |
| F | ALA444 |
| F | SER445 |
| F | SEC489 |
| F | CYS492 |
| F | NI501 |
| F | H2S503 |
| site_id | AE4 |
| Number of Residues | 7 |
| Details | binding site for residue NI F 501 |
| Chain | Residue |
| F | CYS75 |
| F | CSD75 |
| F | CYS78 |
| F | SEC489 |
| F | CYS492 |
| F | FCO500 |
| F | H2S503 |
| site_id | AE5 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 F 502 |
| Chain | Residue |
| F | GLU56 |
| F | ILE441 |
| F | HIS495 |
| F | HOH601 |
| F | HOH610 |
| F | HOH614 |
| site_id | AE6 |
| Number of Residues | 6 |
| Details | binding site for residue CL F 504 |
| Chain | Residue |
| F | CYS78 |
| F | THR80 |
| F | ALA81 |
| F | PHE110 |
| F | ASN113 |
| F | PRO421 |
| site_id | AE7 |
| Number of Residues | 10 |
| Details | binding site for residue SF4 G 301 |
| Chain | Residue |
| G | HIS208 |
| G | CYS211 |
| G | LEU214 |
| G | TYR217 |
| G | CYS232 |
| G | ARG233 |
| G | TYR234 |
| G | CYS238 |
| G | GLY240 |
| G | PRO241 |
| site_id | AE8 |
| Number of Residues | 8 |
| Details | binding site for residue SF4 G 302 |
| Chain | Residue |
| G | THR243 |
| G | CYS247 |
| G | TRP252 |
| G | CYS259 |
| G | CYS265 |
| G | ILE266 |
| G | CYS268 |
| H | ARG182 |
| site_id | AE9 |
| Number of Residues | 13 |
| Details | binding site for residue SF4 G 303 |
| Chain | Residue |
| G | GLY17 |
| G | CYS18 |
| G | CYS21 |
| G | GLU77 |
| G | GLY119 |
| G | THR120 |
| G | CYS121 |
| G | GLY158 |
| G | CYS159 |
| G | PRO160 |
| G | 6ML304 |
| H | ARG73 |
| H | HIS185 |
| site_id | AF1 |
| Number of Residues | 17 |
| Details | binding site for residue 6ML G 304 |
| Chain | Residue |
| G | CYS18 |
| G | THR19 |
| G | GLY20 |
| G | CYS21 |
| G | GLU77 |
| G | GLY78 |
| G | GLY119 |
| G | THR120 |
| G | CYS121 |
| G | GLY158 |
| G | CYS159 |
| G | PRO160 |
| G | PRO161 |
| G | SF4303 |
| G | HOH415 |
| H | ARG73 |
| H | HIS185 |
| site_id | AF2 |
| Number of Residues | 12 |
| Details | binding site for residue FCO H 500 |
| Chain | Residue |
| H | CYS78 |
| H | HIS82 |
| H | ALA420 |
| H | PRO421 |
| H | ARG422 |
| H | LEU425 |
| H | ALA444 |
| H | SER445 |
| H | SEC489 |
| H | CYS492 |
| H | NI501 |
| H | H2S503 |
| site_id | AF3 |
| Number of Residues | 7 |
| Details | binding site for residue NI H 501 |
| Chain | Residue |
| H | CYS75 |
| H | OCS75 |
| H | CYS78 |
| H | SEC489 |
| H | CYS492 |
| H | FCO500 |
| H | H2S503 |
| site_id | AF4 |
| Number of Residues | 6 |
| Details | binding site for residue FE2 H 502 |
| Chain | Residue |
| H | GLU56 |
| H | ILE441 |
| H | HIS495 |
| H | HOH610 |
| H | HOH625 |
| H | HOH675 |
| site_id | AF5 |
| Number of Residues | 6 |
| Details | binding site for residue CL H 504 |
| Chain | Residue |
| H | CYS78 |
| H | THR80 |
| H | ALA81 |
| H | PHE110 |
| H | ASN113 |
| H | PRO421 |
| site_id | AF6 |
| Number of Residues | 14 |
| Details | binding site for residues H2S B 503 and SEC B 489 |
| Chain | Residue |
| B | GLU28 |
| B | CSD75 |
| B | CYS75 |
| B | CYS78 |
| B | ARG422 |
| B | SER445 |
| B | ASP487 |
| B | PRO488 |
| B | LEU490 |
| B | ALA491 |
| B | CYS492 |
| B | ALA493 |
| B | FCO500 |
| B | NI501 |
| site_id | AF7 |
| Number of Residues | 18 |
| Details | binding site for Di-peptide ILE D 74 and CSD D 75 |
| Chain | Residue |
| C | CYS18 |
| D | GLU28 |
| D | ARG53 |
| D | PHE55 |
| D | VAL71 |
| D | GLN72 |
| D | ARG73 |
| D | GLY76 |
| D | VAL77 |
| D | CYS78 |
| D | PRO79 |
| D | HIS82 |
| D | ILE441 |
| D | SEC489 |
| D | ALA491 |
| D | CYS492 |
| D | NI501 |
| D | H2S503 |
| site_id | AF8 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide CSD D 75 and GLY D 76 |
| Chain | Residue |
| C | CYS18 |
| D | GLU28 |
| D | GLN72 |
| D | ARG73 |
| D | ILE74 |
| D | VAL77 |
| D | CYS78 |
| D | PRO79 |
| D | SEC489 |
| D | ALA491 |
| D | CYS492 |
| D | NI501 |
| D | H2S503 |
| D | HOH701 |
| site_id | AF9 |
| Number of Residues | 14 |
| Details | binding site for residues H2S D 503 and SEC D 489 |
| Chain | Residue |
| D | GLU28 |
| D | CSD75 |
| D | CYS75 |
| D | CYS78 |
| D | ARG422 |
| D | SER445 |
| D | ASP487 |
| D | PRO488 |
| D | LEU490 |
| D | ALA491 |
| D | CYS492 |
| D | ALA493 |
| D | FCO500 |
| D | NI501 |
| site_id | AG1 |
| Number of Residues | 18 |
| Details | binding site for Di-peptide ILE F 74 and CSD F 75 |
| Chain | Residue |
| E | CYS18 |
| F | GLU28 |
| F | ARG53 |
| F | PHE55 |
| F | VAL71 |
| F | GLN72 |
| F | ARG73 |
| F | GLY76 |
| F | VAL77 |
| F | CYS78 |
| F | PRO79 |
| F | HIS82 |
| F | ILE441 |
| F | SEC489 |
| F | ALA491 |
| F | CYS492 |
| F | NI501 |
| F | H2S503 |
| site_id | AG2 |
| Number of Residues | 15 |
| Details | binding site for Di-peptide CSD F 75 and GLY F 76 |
| Chain | Residue |
| E | CYS18 |
| F | GLU28 |
| F | GLN72 |
| F | ARG73 |
| F | ILE74 |
| F | VAL77 |
| F | CYS78 |
| F | PRO79 |
| F | PRO184 |
| F | SEC489 |
| F | ALA491 |
| F | CYS492 |
| F | NI501 |
| F | H2S503 |
| F | HOH622 |
| site_id | AG3 |
| Number of Residues | 14 |
| Details | binding site for residues H2S F 503 and SEC F 489 |
| Chain | Residue |
| F | GLU28 |
| F | CSD75 |
| F | CYS75 |
| F | CYS78 |
| F | ARG422 |
| F | SER445 |
| F | ASP487 |
| F | PRO488 |
| F | LEU490 |
| F | ALA491 |
| F | CYS492 |
| F | ALA493 |
| F | FCO500 |
| F | NI501 |
| site_id | AG4 |
| Number of Residues | 17 |
| Details | binding site for Di-peptide ILE H 74 and OCS H 75 |
| Chain | Residue |
| G | CYS18 |
| H | GLU28 |
| H | ARG53 |
| H | PHE55 |
| H | VAL71 |
| H | GLN72 |
| H | ARG73 |
| H | GLY76 |
| H | VAL77 |
| H | CYS78 |
| H | PRO79 |
| H | ILE441 |
| H | SEC489 |
| H | ALA491 |
| H | CYS492 |
| H | NI501 |
| H | H2S503 |
| site_id | AG5 |
| Number of Residues | 14 |
| Details | binding site for Di-peptide OCS H 75 and GLY H 76 |
| Chain | Residue |
| G | CYS18 |
| H | GLU28 |
| H | GLN72 |
| H | ARG73 |
| H | ILE74 |
| H | VAL77 |
| H | CYS78 |
| H | PRO79 |
| H | SEC489 |
| H | ALA491 |
| H | CYS492 |
| H | NI501 |
| H | H2S503 |
| H | HOH633 |
| site_id | AG6 |
| Number of Residues | 14 |
| Details | binding site for residues H2S H 503 and SEC H 489 |
| Chain | Residue |
| H | GLU28 |
| H | CYS75 |
| H | OCS75 |
| H | CYS78 |
| H | ARG422 |
| H | SER445 |
| H | ASP487 |
| H | PRO488 |
| H | LEU490 |
| H | ALA491 |
| H | CYS492 |
| H | ALA493 |
| H | FCO500 |
| H | NI501 |
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. FDPULACav.H |
| Chain | Residue | Details |
| B | PHE486-HIS495 |
