SMTL ID : 2frv.4 (5 other biounits)

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: H.185, C.188, R.190, L.191, C.213, L.214, Y.215, C.219, G.221, P.222, V.240 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.185, A:C.188, A:C.213, A:C.219 SF4.3: 12 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, G.110, T.111, C.112, G.147, C.148, P.149 Chain B: R.63, H.219 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.73 Metal complexes: A:C.17, A:C.20, A:C.112, A:C.148

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

F3S.2: 11 residues within 4Å: Chain A: T.224, N.226, C.228, F.233, W.238, P.239, C.246, I.247, C.249 Chain B: K.216, Q.221 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.228, A:C.246, A:C.249

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

NI.4: 6 residues within 4Å: Chain B: C.65, C.68, C.530, C.533 Ligands: FCO.6, O.7 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:C.65, B:C.68, B:C.530, B:C.533, O.7

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain B: E.46, E.321, L.482, H.536 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.46, B:L.482, B:H.536, H2O.8, H2O.8, H2O.8

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

FCO.6: 14 residues within 4Å: Chain B: C.68, V.71, H.72, A.461, P.462, R.463, L.466, V.484, P.485, S.486, C.530, C.533 Ligands: NI.4, O.7 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.463, B:R.463, B:S.486 Metal complexes: B:C.68, B:C.533, O.7

1 x O: OXYGEN ATOM(Non-covalent)

O.7: 7 residues within 4Å: Chain B: C.65, C.68, R.463, C.530, C.533 Ligands: NI.4, FCO.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:C.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Structure of the [Nife] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands. J.Am.Chem.Soc. (1996)

Release Date

1998-06-17

Peptides

PERIPLASMIC HYDROGENASE: A
PERIPLASMIC HYDROGENASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

PERIPLASMIC HYDROGENASE

PERIPLASMIC HYDROGENASE

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