SMTL ID : 8pow.1

Crystal Structure of the C19G variant of the membrane-bound [NiFe]-Hydrogenase from Cupriavidus necator in the air-oxidized state at 1.61 A Resolution.

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 8 PLIP interactions: 8 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.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.2

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

CL.3: 4 residues within 4Å: Chain A: L.84, R.88, I.98, R.106 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain B: W.118, C.120, G.256 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: P.238 Chain B: G.246 Ligand excluded by PLIP

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

SF4.4: 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.5: 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 ER2: Fe4S4(Non-covalent)

ER2.6: 14 residues within 4Å: Chain A: R.73, H.229 Chain B: E.16, C.17, T.18, G.19, C.20, E.76, S.114, C.115, C.120, G.148, C.149, P.150 6 PLIP interactions: 6 interactions with chain B, Salt bridges: B:E.76 Metal complexes: B:C.17, B:C.20, B:C.115, B:C.120, B:C.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, A. et al., Stepwise conversion of the Cys 6 [4Fe-3S] to a Cys 4 [4Fe-4S] cluster and its impact on the oxygen tolerance of [NiFe]-hydrogenase. Chem Sci (2023)

Release Date

2023-11-15

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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