SMTL ID : 3myr.5 (5 other biounits)

Crystal structure of [NiFe] hydrogenase from Allochromatium vinosum in its Ni-A state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: E.13, C.14, G.16, C.17, D.73, G.111, T.112, C.113, G.146, C.147, P.148 Chain B: R.59, H.214 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.73 Metal complexes: A:C.14, A:C.17, A:C.113, A:C.147 SF4.2: 13 residues within 4Å: Chain A: I.184, H.185, C.188, R.190, R.191, Y.194, C.213, L.214, Y.215, C.219, G.221, P.222, V.241 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.185, A:C.188, A:C.213, A:C.219 SF4.9: 13 residues within 4Å: Chain C: E.13, C.14, G.16, C.17, D.73, G.111, T.112, C.113, G.146, C.147, P.148 Chain D: R.59, H.214 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.73 Metal complexes: C:C.14, C:C.17, C:C.113, C:C.147 SF4.10: 13 residues within 4Å: Chain C: I.184, H.185, C.188, R.190, R.191, Y.194, C.213, L.214, Y.215, C.219, G.221, P.222, V.241 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.185, C:C.188, C:C.213, C:C.219

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

F3S.3: 11 residues within 4Å: Chain A: T.224, N.226, C.228, W.233, W.239, P.240, C.247, L.248, G.249, C.250 Chain B: K.211 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.228, A:C.247, A:C.250 F3S.11: 11 residues within 4Å: Chain C: T.224, N.226, C.228, W.233, W.239, P.240, C.247, L.248, G.249, C.250 Chain D: K.211 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.228, C:C.247, C:C.250

1 x IMD: IMIDAZOLE(Non-covalent)

IMD.4: 5 residues within 4Å: Chain A: M.133, V.141, N.143, Y.173, G.174 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.143

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: I.150, P.151, M.152, N.234, D.235 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain C: I.150, P.151, M.152, N.234, D.235 Ligand excluded by PLIP

2 x NFV: NI-FE OXIDIZED ACTIVE CENTER(Non-covalent)

NFV.6: 13 residues within 4Å: Chain B: C.61, C.64, V.67, H.68, A.485, P.486, R.487, L.490, V.508, P.509, S.510, C.555, C.558 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:C.64, B:R.487, B:R.487, B:S.510 Metal complexes: B:C.61, B:C.64, B:C.64, B:C.555, B:C.558, B:C.558 NFV.12: 13 residues within 4Å: Chain D: C.61, C.64, V.67, H.68, A.485, P.486, R.487, L.490, V.508, P.509, S.510, C.555, C.558 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.487, D:R.487, D:S.510 Metal complexes: D:C.61, D:C.64, D:C.64, D:C.555, D:C.558, D:C.558

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: E.42, A.506, H.561 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.42, B:A.506, B:H.561, H2O.8, H2O.8, H2O.8 MG.13: 3 residues within 4Å: Chain D: E.42, A.506, H.561 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.42, D:A.506, D:H.561, H2O.29, H2O.29, H2O.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ogata, H. et al., The crystal structure of the [NiFe] hydrogenase from the photosynthetic bacterium Allochromatium vinosum: characterization of the oxidized enzyme (Ni-A state). J.Mol.Biol. (2010)

Release Date

2010-08-04

Peptides

Hydrogenase (NiFe) small subunit HydA: AC
Nickel-dependent hydrogenase large subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hydrogenase (NiFe) small subunit HydA

Nickel-dependent hydrogenase large subunit

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