SMTL ID : 5xf9.1 (1 other biounit)

Crystal structure of NAD+-reducing [NiFe]-hydrogenase in the air-oxidized state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.58 Å

Oligo State

hetero-oligomer

Ligands

1 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: G.202, R.203, G.204, A.206, K.213, N.230, D.232, E.233, G.234, Y.314, G.317, E.318, E.319, V.352, N.353, N.354, T.357, G.526, F.527, E.585 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:Y.314, A:Y.314, A:E.318, A:F.527 Hydrogen bonds: A:G.204, A:N.230, A:G.234, A:G.317, A:E.319, A:N.353, A:N.354, A:N.354, A:E.585, A:E.585 Water bridges: A:G.207, A:G.207, A:G.207, A:D.232, A:D.232, A:D.232, A:G.317 Salt bridges: A:K.213

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

SF4.2: 13 residues within 4Å: Chain A: V.315, P.333, 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 SF4.3: 11 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, G.209 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.103, B:C.105, B:C.108, B:C.114 SF4.4: 12 residues within 4Å: Chain B: C.153, I.154, L.155, C.156, G.157, 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 SF4.6: 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 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:E.67 Metal complexes: C:C.24, C:C.27, C:C.95, C:C.159

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

FES.5: 9 residues within 4Å: Chain B: H.41, 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.7: 13 residues within 4Å: Chain D: C.83, S.86, H.87, A.394, P.395, R.396, L.399, V.418, S.419, T.420, C.462, C.465 Ligands: 3NI.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:H.87, D:R.396, D:R.396, D:S.419, D:S.419, D:T.420 Metal complexes: D:C.83, D:C.462, D:C.465

1 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.8: 6 residues within 4Å: Chain D: E.32, C.80, C.83, C.462, C.465 Ligands: FCO.7 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.32, D:C.80, D:C.83, D:C.462, D:C.465

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain D: E.61, L.416, H.468 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.61, D:L.416, D:H.468, H2O.15, H2O.16

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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