SMTL ID : 1yrq.5 (5 other biounits)

Structure of the ready oxidized form of [NiFe]-hydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.184, C.187, R.189, L.190, F.193, C.212, L.213, Y.214, C.218, G.220, P.221, V.239 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.184, A:C.187, A:C.212, A:C.218 SF4.3: 12 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, G.112, T.113, C.114, G.146, C.147, P.148 Chain B: R.70, H.228 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.75 Metal complexes: A:C.17, A:C.20, A:C.114, A:C.147

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

F3S.2: 12 residues within 4Å: Chain A: T.223, N.225, C.227, F.232, W.237, P.238, C.245, L.246, G.247, C.248 Chain B: K.225, Q.230 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.227, A:C.245, A:C.248

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

NI.4: 5 residues within 4Å: Chain B: C.72, C.75, C.543, C.546 Ligands: FCO.6 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.72, B:C.75, B:C.543, B:C.546, H2O.5

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: E.53, L.495, H.549 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.53, B:L.495, B:H.549, H2O.5, H2O.5, H2O.5

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

FCO.6: 13 residues within 4Å: Chain B: C.75, V.78, H.79, A.474, P.475, R.476, L.479, V.497, P.498, S.499, C.543, C.546 Ligands: NI.4 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.476, B:R.476, B:S.499 Metal complexes: B:C.75, B:C.546, H2O.5

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Structural differences between the ready and unready oxidized states of [NiFe] hydrogenases. J.Biol.Inorg.Chem. (2005)

Release Date

2005-04-19

Peptides

Periplasmic [NiFe] hydrogenase small subunit: A
Periplasmic [NiFe] hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
F

B
M

Periplasmic [NiFe] hydrogenase small subunit

Periplasmic [NiFe] hydrogenase large subunit

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