SMTL ID : 4iub.1

Crystal structure of an O2-tolerant [NiFe]-hydrogenase from Ralstonia eutropha in its as-isolated form - oxidized state 1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-1-1-mer

Ligands

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

NFV.1: 13 residues within 4Å: Chain A: C.75, C.78, C.81, H.82, A.528, P.529, R.530, L.533, V.551, P.552, T.553, C.597, C.600 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.530, A:R.530, A:T.553 Metal complexes: A:C.75, A:C.78, A:C.78, A:C.597, A:C.600, A:C.600

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: E.56, C.549, H.603 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.56, A:C.549, A:H.603, H2O.1, H2O.2, H2O.4

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 6 residues within 4Å: Chain A: L.84, R.88, I.98, H.103, R.106, Y.314 8 PLIP interactions: 8 interactions with chain A Water bridges: A:R.88, A:R.88, A:R.106, A:E.107, A:Y.314 Salt bridges: A:R.88, A:H.103, A:R.106 PO4.4: 2 residues within 4Å: Chain A: K.521, R.538 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.538 Salt bridges: A:K.521, A:R.538 PO4.5: 5 residues within 4Å: Chain A: G.501, D.502, T.503, A.504 Chain B: R.211 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.503, A:T.503, A:T.503, A:A.504 Salt bridges: B:R.211 PO4.6: 5 residues within 4Å: Chain A: I.246, G.247, A.248, A.249, S.250 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.247, A:A.248, A:A.249, A:S.250 PO4.7: 2 residues within 4Å: Chain A: T.383, R.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.384 PO4.11: 2 residues within 4Å: Chain B: E.171, L.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.171, B:L.172

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

SF4.8: 12 residues within 4Å: Chain B: H.187, C.190, R.192, R.193, F.196, C.215, L.216, Y.217, C.221, G.223, P.224, I.243 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.187, B:C.190, B:C.215, B:C.221

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

F3S.9: 11 residues within 4Å: Chain A: K.226 Chain B: T.226, N.228, C.230, W.235, P.242, C.249, I.250, G.251, C.252, S.253 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.230, B:C.249, B:C.252

1 x S3F: oxidized [Fe4-S3] cluster(Non-covalent)

S3F.10: 13 residues within 4Å: Chain A: R.73, H.229 Chain B: E.16, C.17, T.18, C.19, C.20, E.76, S.114, C.115, C.120, G.148, C.149 8 PLIP interactions: 8 interactions with chain B, Salt bridges: B:E.76 Metal complexes: B:C.17, B:C.19, B:C.19, B:C.20, B:C.115, B:C.120, B:C.149

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

CL.12: 3 residues within 4Å: Chain B: W.118, C.120, G.256 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frielingsdorf, S. et al., Reversible [4Fe-3S] cluster morphing in an O2-tolerant [NiFe] hydrogenase. Nat.Chem.Biol. (2014)

Release Date

2014-04-02

Peptides

Uptake hydrogenase large subunit: A
Uptake hydrogenase small subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
S

Uptake hydrogenase large subunit

Uptake hydrogenase small subunit

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