SMTL ID : 3c8y.1

1.39 Angstrom crystal structure of Fe-only hydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.39 Å

Oligo State

monomer

Ligands

1 x HCN: 2 IRON/2 SULFUR/3 CARBONYL/2 CYANIDE/WATER/METHYLETHER CLUSTER(Non-covalent)

HCN.1: 19 residues within 4Å: Chain A: A.230, P.231, S.232, I.268, A.272, C.299, S.323, P.324, Q.325, M.353, P.354, C.355, K.358, F.417, G.418, V.423, M.497, C.503 Ligands: SF4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.232, A:Q.325 Metal complexes: A:C.503

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 10 residues within 4Å: Chain A: C.300, P.301, C.355, K.358, M.497, A.498, C.499, C.503, G.506 Ligands: HCN.1 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.300, A:C.355, A:C.499, A:C.503 SF4.3: 14 residues within 4Å: Chain A: L.140, C.157, T.161, T.163, A.165, M.166, F.185, C.190, L.191, L.192, C.193, G.194, Q.195, C.196 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.157, A:C.190, A:C.193, A:C.196 SF4.4: 13 residues within 4Å: Chain A: C.147, L.148, L.149, C.150, G.151, R.152, C.153, I.177, C.200, P.201, V.202, A.204, L.205 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.147, A:C.150, A:C.153, A:C.200 SF4.5: 14 residues within 4Å: Chain A: H.94, E.95, F.96, K.97, C.98, C.101, R.103, R.104, C.107, F.109, L.110, K.146, V.202, A.203 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.94, A:C.98, A:C.101, A:C.107

1 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.6: 10 residues within 4Å: Chain A: A.32, L.33, C.34, F.35, K.45, C.46, E.47, C.49, T.60, C.62 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.34, A:C.46, A:C.49, A:C.62

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: K.223, K.333, K.345, V.347, F.348, L.372, R.373, D.376 Ligands: GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.373 Water bridges: A:K.333, A:K.333 GOL.8: 7 residues within 4Å: Chain A: R.103, R.104, E.105, N.106, C.107, L.110, K.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.104, A:C.107, A:K.111 GOL.9: 5 residues within 4Å: Chain A: N.216, A.217, K.223, F.348 Ligands: GOL.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.216, A:K.223, A:K.223 Water bridges: A:A.217, A:K.223

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pandey, A.S. et al., Dithiomethylether as a ligand in the hydrogenase h-cluster. J.Am.Chem.Soc. (2008)

Release Date

2008-04-22

Peptides

Iron hydrogenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Iron hydrogenase 1

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