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 | 0046872 | molecular_function | metal ion binding |
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 | 0046872 | molecular_function | metal ion binding |
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 | 0046872 | molecular_function | metal ion binding |
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 | 0046872 | molecular_function | metal ion binding |
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 |