SMTL ID : 3ayz.1

Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an air-oxidized condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FE2: FE (II) ION(Non-covalent)

FE2.1: 10 residues within 4Å: Chain A: C.79, C.593 Ligands: 3NI.2, CMO.3, CYN.4, CYN.5, O.6, O.7, O.9, O.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:C.79, A:C.593, CMO.3, O.6 FE2.19: 10 residues within 4Å: Chain C: C.79, C.593 Ligands: 3NI.20, CMO.21, CYN.22, CYN.23, O.24, O.25, O.27, O.28 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:C.79, C:C.593, CMO.21, O.24

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

3NI.2: 10 residues within 4Å: Chain A: C.76, C.79, C.590, C.593 Ligands: FE2.1, O.6, O.7, O.8, O.9, O.10 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:C.76, A:C.79, A:C.590, O.6, O.7 3NI.20: 11 residues within 4Å: Chain C: C.76, C.79, C.590, C.593 Ligands: FE2.19, CYN.23, O.24, O.25, O.26, O.27, O.28 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Ligand interactions Metal complexes: C:C.76, C:C.79, C:C.590, O.24, O.25

2 x CMO: CARBON MONOXIDE(Non-functional Binders)

CMO.3: 11 residues within 4Å: Chain A: C.79, C.82, H.83, A.521, L.526, P.545, C.593 Ligands: FE2.1, CYN.4, CYN.5, O.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.83 CMO.21: 12 residues within 4Å: Chain C: C.79, C.82, H.83, A.521, L.526, V.544, P.545, C.593 Ligands: FE2.19, CYN.22, CYN.23, O.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.83

4 x CYN: CYANIDE ION(Non-covalent)

CYN.4: 8 residues within 4Å: Chain A: C.79, A.521, P.522, R.523 Ligands: FE2.1, CMO.3, CYN.5, O.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.523, A:R.523 CYN.5: 10 residues within 4Å: Chain A: R.523, V.544, P.545, T.546, C.590, C.593 Ligands: FE2.1, CMO.3, CYN.4, O.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.546, A:T.546 CYN.22: 8 residues within 4Å: Chain C: C.79, A.521, P.522, R.523 Ligands: FE2.19, CMO.21, CYN.23, O.24 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.523, C:R.523 CYN.23: 11 residues within 4Å: Chain C: R.523, V.544, P.545, T.546, C.590, C.593 Ligands: FE2.19, 3NI.20, CMO.21, CYN.22, O.24 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.546

10 x O: OXYGEN ATOM(Non-covalent)(Covalent)

O.6: 14 residues within 4Å: Chain A: C.76, C.79, R.523, C.590, C.593 Ligands: FE2.1, 3NI.2, CMO.3, CYN.4, CYN.5, O.7, O.8, O.9, O.10 No protein-ligand interaction detected (PLIP) O.7: 11 residues within 4Å: Chain A: E.28, C.76, C.590, A.592, C.593 Ligands: FE2.1, 3NI.2, O.6, O.8, O.9, O.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.593 O.8: 10 residues within 4Å: Chain A: E.28, C.76, C.590, L.591, A.592, C.593 Ligands: 3NI.2, O.6, O.7, O.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.592, A:C.593 O.9: 9 residues within 4Å: Chain A: C.76, C.79, C.590, C.593 Ligands: FE2.1, 3NI.2, O.6, O.7, O.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.78, A:C.79 O.10: 10 residues within 4Å: Chain A: C.76, C.79, C.590, C.593 Ligands: FE2.1, 3NI.2, O.6, O.7, O.8, O.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.593 O.24: 14 residues within 4Å: Chain C: C.76, C.79, R.523, C.590, C.593 Ligands: FE2.19, 3NI.20, CMO.21, CYN.22, CYN.23, O.25, O.26, O.27, O.28 No protein-ligand interaction detected (PLIP) O.25: 11 residues within 4Å: Chain C: E.28, C.76, C.590, A.592, C.593 Ligands: FE2.19, 3NI.20, O.24, O.26, O.27, O.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.28, C:C.593 O.26: 10 residues within 4Å: Chain C: E.28, C.76, C.590, L.591, A.592, C.593 Ligands: 3NI.20, O.24, O.25, O.28 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.28, C:A.592, C:C.593 O.27: 9 residues within 4Å: Chain C: C.76, C.79, C.590, C.593 Ligands: FE2.19, 3NI.20, O.24, O.25, O.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:V.78, C:C.79 O.28: 11 residues within 4Å: Chain C: E.28, C.76, C.79, C.590, C.593 Ligands: FE2.19, 3NI.20, O.24, O.25, O.26, O.27 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.28, C:C.593

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 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.12: 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: 1 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.220, A:I.244, A:D.245, A:G.246, A:S.496, A:S.496 GOL.29: 6 residues within 4Å: Chain C: K.310, Q.319, Y.426, Y.475, D.478, D.482 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:K.310, C:Q.319, C:Y.475, C:D.478 Water bridges: C:Q.319, C:Y.426, C:D.482 GOL.30: 7 residues within 4Å: Chain C: I.242, N.243, I.244, D.245, G.246, S.496 Chain D: R.220 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:I.244, C:D.245, C:S.496, C:S.496, D:R.220

2 x MG: MAGNESIUM ION(Non-covalent)

MG.13: 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.1, H2O.9, H2O.12 MG.18: 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.40, H2O.41, H2O.41

4 x F4S: FE4-S3 CLUSTER(Non-covalent)

F4S.14: 12 residues within 4Å: Chain A: R.74 Chain B: C.23, T.24, C.25, C.26, E.82, S.120, C.121, C.126, G.157, C.158 Ligands: SF3.15 8 PLIP interactions: 8 interactions with chain B, Salt bridges: B:E.82 Metal complexes: B:C.23, B:C.25, B:C.25, B:C.26, B:C.121, B:C.126, B:C.158 F4S.15: 12 residues within 4Å: Chain A: R.74 Chain B: C.23, T.24, C.25, C.26, E.82, S.120, C.121, C.126, G.157, C.158 Ligands: F4S.14 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Salt bridges: B:E.82 Metal complexes: B:C.23, B:C.25, B:C.25, B:C.26, B:C.121, B:C.126, B:C.158, SF3.15 F4S.31: 13 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 Ligands: SF3.32 9 PLIP interactions: 9 interactions with chain D, Salt bridges: D:E.22, D:E.82 Metal complexes: D:C.23, D:C.25, D:C.25, D:C.26, D:C.121, D:C.126, D:C.158 F4S.32: 13 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 Ligands: F4S.31 10 PLIP interactions: 9 interactions with chain D, 1 Ligand-Ligand interactions Salt bridges: D:E.22, D:E.82 Metal complexes: D:C.23, D:C.25, D:C.25, D:C.26, D:C.121, D:C.126, D:C.158, SF3.32

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

F3S.16: 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.33: 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)

SF4.17: 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 SF4.34: 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

2011-10-12

Peptides

Membrane-bound hydrogenase large subunit: AC
Membrane-bound hydrogenase small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Membrane-bound hydrogenase large subunit

Membrane-bound hydrogenase small subunit

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