SMTL ID : 5byr.2 (1 other biounit)

Semisynthetic [FeFe]-hydrogenase CpI with propane-dithiolato-bridged [2Fe] cofactor

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: C.193, C.300, P.301, G.302, P.354, C.355, S.357, K.358, M.497, A.498, C.499, G.502, C.503, G.506 Ligands: 4WW.6 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.300, A:C.355, A:C.499, A:C.503 SF4.2: 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 SF4.3: 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 SF4.4: 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.5: 12 residues within 4Å: Chain A: A.32, L.33, C.34, F.35, N.40, K.45, C.46, E.47, I.48, 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

1 x 4WW: bis(cyanido-kappaC)(dicarbonyl)-mu-(oxomethylidene)[mu-propane-1,3-bis(thiolate)-1kappa~2~S~1~,S~3~:2kappa~2~S~1~,S~3~] diiron(2+)(Non-covalent)

4WW.6: 20 residues within 4Å: Chain A: A.230, P.231, S.232, I.268, A.272, C.299, C.300, 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: SF4.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.423 Hydrogen bonds: A:S.232, A:Q.325, A:K.358 Metal complexes: A:C.503

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain A: L.218, A.220, D.263 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:L.218, H2O.1, H2O.2, H2O.4, H2O.8, H2O.9 MG.8: 2 residues within 4Å: Chain A: N.40, D.42 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.42, H2O.5, H2O.7, H2O.8, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Esselborn, J. et al., A structural view of synthetic cofactor integration into [FeFe]-hydrogenases. Chem Sci (2016)

Release Date

2015-11-11

Peptides

Iron hydrogenase 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Iron hydrogenase 1

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