SMTL ID : 3ze9.1

3D structure of the NiFeSe hydrogenase from D. vulgaris Hildenborough in the oxidized as-isolated state at 1.33 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.207, H.208, C.211, Y.213, L.214, Y.217, C.232, R.233, Y.234, C.238, G.240, P.241, V.260 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.208, A:C.211, A:C.232, A:C.238, SF4.1, SF4.1 SF4.2: 16 residues within 4Å: Chain A: W.165, I.207, T.243, A.245, C.247, W.252, W.258, C.259, V.260, C.265, I.266, G.267, C.268, V.269 Chain B: R.171, Q.176 7 PLIP interactions: 4 interactions with chain A, 3 Ligand-Ligand interactions Metal complexes: A:C.247, A:C.259, A:C.265, A:C.268, SF4.2, SF4.2, SF4.2

1 x FSX: BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)(Covalent)

FSX.3: 16 residues within 4Å: Chain A: G.17, C.18, T.19, G.20, C.21, E.77, G.78, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.62, H.174 14 PLIP interactions: 11 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:C.18, A:T.19, A:G.20, A:E.77, A:E.77, A:G.78 Water bridges: A:C.121 Metal complexes: A:C.18, A:E.77, A:C.121, A:C.159, FSX.3, FSX.3, FSX.3

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

FCO.4: 12 residues within 4Å: Chain B: C.67, H.71, A.409, P.410, R.411, L.414, S.432, A.433, S.434, U.478, C.481 Ligands: NI.5 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.411, B:R.411, B:A.433, B:S.434 Metal complexes: B:C.67, B:C.481

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

NI.5: 6 residues within 4Å: Chain B: C.64, C.67, R.411, U.478, C.481 Ligands: FCO.4 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.67, B:C.481

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

FE2.6: 4 residues within 4Å: Chain B: E.45, K.306, I.430, H.484 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.45, B:I.430, B:H.484, H2O.15, H2O.16, H2O.24

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

CL.7: 6 residues within 4Å: Chain B: C.67, T.69, A.70, F.99, N.102, P.410 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques, M.C. et al., Redox State-Dependent Changes in the Crystal Structure of [Nifese] Hydrogenase from Desulfovibrio Vulgaris Hildenborough. Int.J.Hydrogen Energy (2013)

Release Date

2013-06-12

Peptides

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT: A
PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PERIPLASMIC [NIFESE] HYDROGENASE, SMALL SUBUNIT

PERIPLASMIC [NIFESE] HYDROGENASE, LARGE SUBUNIT, SELENOCYSTEINE-CONTAINING

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