SMTL ID : 5jsy.1

The 3D structure of the Ni-reconstituted U489C variant of [NiFeSe] hydrogenase from Desulfovibrio vulgaris Hildenborough at 1.04 Angstrom resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.04 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.241, H.242, C.245, Y.247, L.248, Y.251, C.266, R.267, Y.268, C.272, G.274, P.275, V.294 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.242, A:C.245, A:C.266, A:C.272 SF4.2: 16 residues within 4Å: Chain A: W.199, I.241, T.277, A.279, C.281, W.286, W.292, C.293, V.294, C.299, I.300, G.301, C.302, V.303 Chain B: R.179, Q.184 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.281, A:C.293, A:C.299, A:C.302 SF4.3: 15 residues within 4Å: Chain A: G.51, C.52, G.54, C.55, E.111, G.112, G.153, T.154, C.155, G.192, C.193, P.194, P.195 Chain B: R.70, H.182 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.111 Metal complexes: A:C.52, A:C.55, A:C.155, A:C.193

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

FCO.4: 13 residues within 4Å: Chain B: C.75, H.79, A.417, P.418, R.419, L.422, S.440, A.441, S.442, C.486, C.489 Ligands: NI.5, H2S.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.419, B:R.419, B:A.441, B:S.442 Metal complexes: B:C.75, B:C.489

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

NI.5: 8 residues within 4Å: Chain B: C.72, V.74, C.75, R.419, C.486, C.489 Ligands: FCO.4, H2S.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.72, B:C.75, B:C.489

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

FE2.6: 4 residues within 4Å: Chain B: E.53, K.314, I.438, H.492 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.53, B:I.438, B:H.492, H2O.15, H2O.16, H2O.17

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.7: 8 residues within 4Å: Chain B: C.72, V.74, C.75, R.419, C.486, C.489 Ligands: FCO.4, NI.5 No protein-ligand interaction detected (PLIP)

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

CL.8: 6 residues within 4Å: Chain B: C.75, T.77, A.78, F.107, N.110, P.418 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Marques, M.C. et al., The direct role of selenocysteine in [NiFeSe] hydrogenase maturation and catalysis. Nat. Chem. Biol. (2017)

Release Date

2017-03-22

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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