SMTL ID : 5y34.1

Membrane-bound respiratory [NiFe]-hydrogenase from Hydrogenovibrio marinus in a ferricyanide-oxidized condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

hetero-2-2-mer

Ligands

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

3NI.1: 6 residues within 4Å: Chain A: C.76, C.79, C.590, C.593 Ligands: FCO.2, O.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.76, A:C.79, A:C.590, A:C.593, O.3 3NI.11: 6 residues within 4Å: Chain C: C.76, C.79, C.590, C.593 Ligands: FCO.12, O.13 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.76, C:C.79, C:C.590, C:C.593, O.13

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

FCO.2: 14 residues within 4Å: Chain A: C.79, C.82, H.83, A.521, P.522, R.523, L.526, V.544, P.545, T.546, C.590, C.593 Ligands: 3NI.1, O.3 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.523, A:R.523, A:T.546, A:T.546 Metal complexes: A:C.79, A:C.593, O.3 FCO.12: 14 residues within 4Å: Chain C: C.79, C.82, H.83, A.521, P.522, R.523, L.526, V.544, P.545, T.546, C.590, C.593 Ligands: 3NI.11, O.13 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:R.523, C:R.523, C:T.546 Metal complexes: C:C.79, C:C.593, O.13

2 x O: OXYGEN ATOM(Non-covalent)

O.3: 7 residues within 4Å: Chain A: C.76, C.79, R.523, C.590, C.593 Ligands: 3NI.1, FCO.2 No protein-ligand interaction detected (PLIP) O.13: 7 residues within 4Å: Chain C: C.76, C.79, R.523, C.590, C.593 Ligands: 3NI.11, FCO.12 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.310, Q.319, Y.475, D.478, D.482 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.310, A:Q.319, A:D.478 Water bridges: A:Q.319, A:D.482 GOL.5: 7 residues within 4Å: Chain A: I.242, N.243, I.244, D.245, G.246, S.496 Chain B: R.220 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:I.244, A:D.245, A:G.246, A:S.496, A:S.496, B:R.220 GOL.14: 5 residues within 4Å: Chain C: K.310, Q.319, Y.475, D.478, D.482 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:K.310, C:Q.319, C:Y.475, C:D.478 Water bridges: C:Q.319, C:D.482 GOL.15: 7 residues within 4Å: Chain C: I.242, N.243, I.244, D.245, G.246, S.496 Chain D: R.220 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:I.244, C:D.245, C:G.246, C:S.496, C:S.496 Water bridges: C:D.245, C:D.245

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 3 residues within 4Å: Chain A: E.57, C.542, H.596 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.57, A:C.542, A:H.596, H2O.2, H2O.2, H2O.2 MG.10: 3 residues within 4Å: Chain C: E.57, C.542, H.596 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.57, C:C.542, C:H.596, H2O.45, H2O.45, H2O.45

2 x SF3: FE4-S3 CLUSTER(Non-covalent)

SF3.7: 12 residues within 4Å: Chain A: R.74 Chain B: E.22, C.23, T.24, C.25, C.26, E.82, S.120, C.121, C.126, G.157, C.158 10 PLIP interactions: 10 interactions with chain B, Salt bridges: B:E.22, B:E.82 Metal complexes: B:C.23, B:C.25, B:C.25, B:C.26, B:E.82, B:C.121, B:C.126, B:C.158 SF3.16: 12 residues within 4Å: Chain C: R.74 Chain D: E.22, C.23, T.24, C.25, C.26, E.82, S.120, C.121, C.126, G.157, C.158 9 PLIP interactions: 9 interactions with chain D, Salt bridges: D:E.82 Metal complexes: D:C.23, D:C.25, D:C.25, D:C.26, D:E.82, D:C.121, D:C.126, D:C.158

2 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.8: 11 residues within 4Å: Chain A: K.227 Chain B: T.235, N.237, C.239, W.244, P.251, C.258, I.259, G.260, C.261, S.262 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.239, B:C.258, B:C.261 F3S.17: 11 residues within 4Å: Chain C: K.227 Chain D: T.235, N.237, C.239, W.244, P.251, C.258, I.259, G.260, C.261, S.262 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.239, D:C.258, D:C.261

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

SF4.9: 12 residues within 4Å: Chain B: H.196, C.199, R.201, R.202, F.205, C.224, L.225, Y.226, C.230, G.232, P.233, I.252 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.196, B:C.199, B:C.224, B:C.230 SF4.18: 12 residues within 4Å: Chain D: H.196, C.199, R.201, R.202, F.205, C.224, L.225, Y.226, C.230, G.232, P.233, I.252 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.196, D:C.199, D:C.224, D:C.230

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shomura, Y. et al., Structural basis for a [4Fe-3S] cluster in the oxygen-tolerant membrane-bound [NiFe]-hydrogenase. Nature (2011)

Release Date

2017-08-16

Peptides

Hydrogenase: AC
Membrane-bound hydrogenase small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hydrogenase

Membrane-bound hydrogenase small subunit

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