4KO3
Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air
Functional Information from GO Data
Chain | GOid | namespace | contents |
L | 0008901 | molecular_function | ferredoxin hydrogenase activity |
L | 0016151 | molecular_function | nickel cation binding |
L | 0016491 | molecular_function | oxidoreductase activity |
L | 0046872 | molecular_function | metal ion binding |
M | 0008901 | molecular_function | ferredoxin hydrogenase activity |
M | 0016151 | molecular_function | nickel cation binding |
M | 0016491 | molecular_function | oxidoreductase activity |
M | 0046872 | molecular_function | metal ion binding |
S | 0008901 | molecular_function | ferredoxin hydrogenase activity |
S | 0009055 | molecular_function | electron transfer activity |
S | 0009061 | biological_process | anaerobic respiration |
S | 0009375 | cellular_component | ferredoxin hydrogenase complex |
S | 0016020 | cellular_component | membrane |
S | 0016491 | molecular_function | oxidoreductase activity |
S | 0033748 | molecular_function | hydrogenase (acceptor) activity |
S | 0042597 | cellular_component | periplasmic space |
S | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
S | 0046872 | molecular_function | metal ion binding |
S | 0051536 | molecular_function | iron-sulfur cluster binding |
S | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
T | 0008901 | molecular_function | ferredoxin hydrogenase activity |
T | 0009055 | molecular_function | electron transfer activity |
T | 0009061 | biological_process | anaerobic respiration |
T | 0009375 | cellular_component | ferredoxin hydrogenase complex |
T | 0016020 | cellular_component | membrane |
T | 0016491 | molecular_function | oxidoreductase activity |
T | 0033748 | molecular_function | hydrogenase (acceptor) activity |
T | 0042597 | cellular_component | periplasmic space |
T | 0044569 | cellular_component | [Ni-Fe] hydrogenase complex |
T | 0046872 | molecular_function | metal ion binding |
T | 0051536 | molecular_function | iron-sulfur cluster binding |
T | 0051539 | molecular_function | 4 iron, 4 sulfur cluster binding |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE SF4 S 301 |
Chain | Residue |
S | HIS208 |
S | CYS211 |
S | CYS231 |
S | LYS232 |
S | ALA233 |
S | CYS237 |
S | VAL259 |
site_id | AC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 S 302 |
Chain | Residue |
S | THR242 |
S | CYS246 |
S | TRP251 |
S | CYS258 |
S | CYS264 |
S | ILE265 |
S | CYS267 |
L | ARG185 |
L | GLN190 |
site_id | AC3 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 S 303 |
Chain | Residue |
L | ARG68 |
L | HIS188 |
S | GLY17 |
S | CYS18 |
S | CYS21 |
S | GLY124 |
S | THR125 |
S | CYS126 |
S | GLY163 |
S | CYS164 |
S | PRO165 |
site_id | AC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA S 304 |
Chain | Residue |
L | ASP87 |
S | GLU152 |
S | HOH454 |
S | HOH455 |
S | HOH457 |
S | HOH471 |
site_id | AC5 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CL S 305 |
Chain | Residue |
S | HIS167 |
S | ASN252 |
S | ASN253 |
S | HOH403 |
S | HOH431 |
S | HOH458 |
site_id | AC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL S 306 |
Chain | Residue |
M | ASP39 |
M | ARG455 |
M | HOH1000 |
S | HIS30 |
S | ARG32 |
S | HOH519 |
S | HOH566 |
site_id | AC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL S 307 |
Chain | Residue |
L | ASP413 |
L | HOH950 |
S | TYR62 |
S | ASP112 |
S | LYS116 |
S | HOH547 |
S | HOH557 |
S | HOH675 |
site_id | AC8 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA S 308 |
Chain | Residue |
L | HOH901 |
L | HOH1095 |
S | HOH539 |
S | HOH634 |
S | HOH652 |
S | HOH767 |
site_id | AC9 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE FCO L 501 |
Chain | Residue |
L | CYS73 |
L | HIS77 |
L | ALA423 |
L | PRO424 |
L | ARG425 |
L | ALA447 |
L | THR448 |
L | CYS495 |
L | NI502 |
L | HOH607 |
site_id | BC1 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE NI L 502 |
Chain | Residue |
L | CYS70 |
L | CYS73 |
L | SE7492 |
L | GLY494 |
L | CYS495 |
L | FCO501 |
L | HOH607 |
L | HOH608 |
site_id | BC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA L 503 |
Chain | Residue |
L | GLU51 |
L | ILE444 |
L | HIS498 |
L | HOH609 |
L | HOH610 |
L | HOH611 |
site_id | BC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE H2S L 504 |
Chain | Residue |
L | CYS73 |
L | THR75 |
L | ALA76 |
L | PHE105 |
L | ASN108 |
L | PRO424 |
site_id | BC4 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE SF4 T 301 |
Chain | Residue |
T | HIS208 |
T | CYS211 |
T | TYR213 |
T | LEU214 |
T | CYS231 |
T | LYS232 |
T | CYS237 |
T | GLY239 |
T | VAL259 |
site_id | BC5 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE SF4 T 302 |
Chain | Residue |
M | ARG185 |
T | THR242 |
T | CYS246 |
T | TRP251 |
T | CYS258 |
T | CYS264 |
T | ILE265 |
T | CYS267 |
site_id | BC6 |
Number of Residues | 11 |
Details | BINDING SITE FOR RESIDUE SF4 T 303 |
Chain | Residue |
M | ARG68 |
M | HIS188 |
T | GLY17 |
T | CYS18 |
T | CYS21 |
T | GLY124 |
T | THR125 |
T | CYS126 |
T | GLY163 |
T | CYS164 |
T | PRO165 |
site_id | BC7 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA T 304 |
Chain | Residue |
M | HOH615 |
M | HOH620 |
T | HOH506 |
T | HOH528 |
T | HOH538 |
T | HOH547 |
T | HOH580 |
site_id | BC8 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA T 305 |
Chain | Residue |
L | HOH856 |
T | ASP271 |
T | GLY275 |
T | HOH469 |
T | HOH499 |
T | HOH728 |
T | HOH746 |
site_id | BC9 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA T 306 |
Chain | Residue |
T | ASP195 |
T | ASP196 |
T | HOH475 |
T | HOH582 |
T | HOH724 |
T | HOH732 |
site_id | CC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE FCO M 501 |
Chain | Residue |
M | CYS73 |
M | HIS77 |
M | ALA423 |
M | PRO424 |
M | ARG425 |
M | ALA447 |
M | THR448 |
M | CYS495 |
M | NI502 |
M | HOH623 |
site_id | CC2 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE NI M 502 |
Chain | Residue |
M | GLU23 |
M | CYS70 |
M | CYS73 |
M | SE7492 |
M | GLY494 |
M | CYS495 |
M | FCO501 |
M | HOH623 |
M | HOH624 |
site_id | CC3 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE CA M 503 |
Chain | Residue |
M | GLU51 |
M | ILE444 |
M | HIS498 |
M | HOH625 |
M | HOH626 |
M | HOH627 |
site_id | CC4 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE H2S M 504 |
Chain | Residue |
M | CYS73 |
M | THR75 |
M | ALA76 |
M | PHE105 |
M | ASN108 |
M | PRO424 |
site_id | CC5 |
Number of Residues | 2 |
Details | BINDING SITE FOR RESIDUE GOL M 505 |
Chain | Residue |
M | THR157 |
M | HOH1024 |
site_id | CC6 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL M 506 |
Chain | Residue |
M | ASP39 |
M | ARG455 |
M | GLY459 |
M | ARG461 |
S | GLU35 |
site_id | CC7 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE CA M 507 |
Chain | Residue |
M | ASP17 |
M | HIS25 |
M | LEU26 |
M | HOH767 |
T | HOH593 |
Functional Information from PROSITE/UniProt
site_id | PS00507 |
Number of Residues | 26 |
Details | NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGFEqilrgrdprdssqivQRiCGVC |
Chain | Residue | Details |
L | ARG48-CYS73 |
site_id | PS00508 |
Number of Residues | 10 |
Details | NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. YDPULGCav.H |
Chain | Residue | Details |
L | TYR489-HIS498 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 24 |
Details | BINDING: |
Chain | Residue | Details |
S | CYS246 | |
S | CYS258 | |
S | CYS264 | |
S | CYS267 | |
T | CYS18 | |
T | CYS21 | |
T | CYS126 | |
T | CYS164 | |
T | HIS208 | |
T | CYS211 | |
T | CYS231 | |
T | CYS237 | |
T | CYS246 | |
T | CYS258 | |
T | CYS264 | |
T | CYS267 | |
S | CYS18 | |
S | CYS21 | |
S | CYS126 | |
S | CYS164 | |
S | HIS208 | |
S | CYS211 | |
S | CYS231 | |
S | CYS237 |
Catalytic Information from CSA
site_id | MCSA1 |
Number of Residues | 12 |
Details | M-CSA 443 |
Chain | Residue | Details |
S | CYS18 | metal ligand |
S | CYS21 | metal ligand |
S | CYS126 | metal ligand |
S | CYS164 | metal ligand |
S | HIS208 | metal ligand |
S | CYS211 | metal ligand |
S | CYS231 | metal ligand |
S | CYS237 | metal ligand |
S | CYS246 | metal ligand |
S | CYS258 | metal ligand |
S | CYS264 | metal ligand |
S | CYS267 | metal ligand |
site_id | MCSA2 |
Number of Residues | 12 |
Details | M-CSA 443 |
Chain | Residue | Details |
T | CYS18 | metal ligand |
T | CYS21 | metal ligand |
T | CYS126 | metal ligand |
T | CYS164 | metal ligand |
T | HIS208 | metal ligand |
T | CYS211 | metal ligand |
T | CYS231 | metal ligand |
T | CYS237 | metal ligand |
T | CYS246 | metal ligand |
T | CYS258 | metal ligand |
T | CYS264 | metal ligand |
T | CYS267 | metal ligand |