4KN9
High-resolution structure of H2-activated 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 | 6 |
| Details | BINDING SITE FOR RESIDUE SF4 S 301 |
| Chain | Residue |
| S | HIS208 |
| S | CYS211 |
| S | CYS231 |
| S | LYS232 |
| S | CYS237 |
| S | VAL259 |
| site_id | AC2 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 S 302 |
| Chain | Residue |
| S | TRP251 |
| S | CYS258 |
| S | CYS264 |
| S | ILE265 |
| S | CYS267 |
| L | ARG185 |
| S | THR242 |
| S | CYS246 |
| 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 | HOH455 |
| S | HOH456 |
| S | HOH458 |
| S | HOH472 |
| site_id | AC5 |
| Number of Residues | 5 |
| Details | BINDING SITE FOR RESIDUE CL S 305 |
| Chain | Residue |
| S | ASN27 |
| S | HIS167 |
| S | ASN253 |
| S | HOH432 |
| S | HOH459 |
| site_id | AC6 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL S 306 |
| Chain | Residue |
| M | ASP39 |
| M | ARG455 |
| M | HOH986 |
| S | HIS30 |
| S | ARG32 |
| S | HOH519 |
| S | HOH566 |
| site_id | AC7 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE GOL S 307 |
| Chain | Residue |
| L | ASP413 |
| L | HOH948 |
| 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 | HOH899 |
| L | HOH1091 |
| S | HOH539 |
| S | HOH633 |
| S | HOH651 |
| S | HOH753 |
| site_id | AC9 |
| Number of Residues | 11 |
| 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 | SEC492 |
| L | CYS495 |
| L | NI502 |
| L | HOH607 |
| site_id | BC1 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI L 502 |
| Chain | Residue |
| L | CYS70 |
| L | CYS73 |
| L | SEC492 |
| L | CYS495 |
| L | FCO501 |
| L | HOH607 |
| site_id | BC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA L 503 |
| Chain | Residue |
| L | GLU51 |
| L | ILE444 |
| L | HIS498 |
| L | HOH608 |
| L | HOH609 |
| L | HOH610 |
| 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 | 10 |
| Details | BINDING SITE FOR RESIDUE SF4 T 301 |
| Chain | Residue |
| T | HIS208 |
| T | CYS211 |
| T | TYR213 |
| T | LEU214 |
| T | CYS231 |
| T | LYS232 |
| T | ALA233 |
| T | CYS237 |
| T | GLY239 |
| T | VAL259 |
| site_id | BC5 |
| Number of Residues | 8 |
| Details | BINDING SITE FOR RESIDUE SF4 T 302 |
| Chain | Residue |
| T | CYS258 |
| T | CYS264 |
| T | ILE265 |
| T | CYS267 |
| M | ARG185 |
| T | THR242 |
| T | CYS246 |
| T | TRP251 |
| 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 | HOH609 |
| M | HOH612 |
| T | HOH506 |
| T | HOH530 |
| T | HOH540 |
| T | HOH549 |
| T | HOH582 |
| site_id | BC8 |
| Number of Residues | 7 |
| Details | BINDING SITE FOR RESIDUE CA T 305 |
| Chain | Residue |
| L | HOH854 |
| T | ASP271 |
| T | GLY275 |
| T | HOH469 |
| T | HOH499 |
| T | HOH724 |
| T | HOH735 |
| site_id | BC9 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA T 306 |
| Chain | Residue |
| T | ASP195 |
| T | ASP196 |
| T | HOH475 |
| T | HOH584 |
| T | HOH721 |
| T | HOH727 |
| site_id | CC1 |
| Number of Residues | 11 |
| 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 | SEC492 |
| M | CYS495 |
| M | NI502 |
| M | HOH616 |
| site_id | CC2 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE NI M 502 |
| Chain | Residue |
| M | CYS70 |
| M | CYS73 |
| M | SEC492 |
| M | CYS495 |
| M | FCO501 |
| M | HOH616 |
| site_id | CC3 |
| Number of Residues | 6 |
| Details | BINDING SITE FOR RESIDUE CA M 503 |
| Chain | Residue |
| M | GLU51 |
| M | ILE444 |
| M | HIS498 |
| M | HOH617 |
| M | HOH618 |
| M | HOH619 |
| 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 | 6 |
| Details | BINDING SITE FOR RESIDUE GOL M 505 |
| Chain | Residue |
| M | ASP39 |
| M | ARG455 |
| M | GLY459 |
| M | HOH654 |
| M | HOH851 |
| S | GLU35 |
| site_id | CC6 |
| Number of Residues | 1 |
| Details | BINDING SITE FOR RESIDUE GOL M 506 |
| Chain | Residue |
| M | HOH1010 |
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 |
