SMTL ID : 5xfa.1 (1 other biounit)

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the H2-reduced state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: S.478, C.479, G.480, F.481, C.482, C.485, S.523, N.524, C.525, F.527, G.528 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.479, A:C.482, A:C.485, A:C.525 SF4.2: 12 residues within 4Å: Chain B: F.98, H.103, F.104, C.105, C.108, K.110, S.111, C.114, L.116, Q.117, V.208, G.209 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.103, B:C.105, B:C.108, B:C.114 SF4.3: 13 residues within 4Å: Chain B: C.153, I.154, L.155, C.156, G.157, L.158, C.159, L.182, C.206, P.207, V.208, A.210, L.211 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.153, B:C.156, B:C.159, B:C.206 SF4.5: 13 residues within 4Å: Chain C: G.23, C.24, G.26, C.27, E.67, G.93, A.94, C.95, G.158, C.159, P.160 Chain D: R.78, H.183 7 PLIP interactions: 5 interactions with chain C, 2 Ligand-Water interactions, Salt bridges: C:E.67 Metal complexes: C:C.24, C:C.27, C:C.95, C:C.159, H2O.2, H2O.2

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

FES.4: 10 residues within 4Å: Chain B: H.41, L.42, C.43, W.44, G.52, S.53, C.54, R.55, C.57, C.69 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.43, B:C.54, B:C.57, B:C.69

1 x FCO: CARBONMONOXIDE-(DICYANO) IRON(Non-covalent)

FCO.6: 12 residues within 4Å: Chain D: C.83, H.87, A.394, P.395, R.396, L.399, V.418, S.419, T.420, C.462, C.465 Ligands: NI.7 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:R.396, D:R.396, D:S.419, D:S.419, D:T.420 Metal complexes: D:C.83, D:C.465

1 x NI: NICKEL (II) ION(Non-covalent)

NI.7: 5 residues within 4Å: Chain D: C.80, C.83, C.462, C.465 Ligands: FCO.6 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.80, D:C.83, D:C.462, D:C.465

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain D: E.61, E.285, L.416, H.468 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.61, D:L.416, D:H.468, H2O.3, H2O.3, H2O.3

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shomura, Y. et al., Structural basis of the redox switches in the NAD(+)-reducing soluble [NiFe]-hydrogenase. Science (2017)

Release Date

2017-08-23

Peptides

NAD-reducing hydrogenase: A
NAD-reducing hydrogenase: B
NAD-reducing hydrogenase: C
NAD-reducing hydrogenase: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NAD-reducing hydrogenase

NAD-reducing hydrogenase

NAD-reducing hydrogenase

NAD-reducing hydrogenase

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