SMTL ID : 6ruc.1

THE 3D STRUCTURE OF [NIFESE] HYDROGENASE G491S VARIANT FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.20 ANGSTROM RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 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.207, H.208, C.211, Y.213, L.214, Y.217, C.232, R.233, Y.234, C.238, G.240, P.241, V.260 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.208, A:C.211, A:C.232, A:C.238 SF4.2: 16 residues within 4Å: Chain A: W.165, I.207, T.243, A.245, C.247, W.252, W.258, C.259, V.260, C.265, I.266, G.267, C.268, V.269 Chain B: R.179, Q.184 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.247, A:C.259, A:C.265, A:C.268 SF4.3: 16 residues within 4Å: Chain A: G.17, C.18, T.19, G.20, C.21, E.77, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.70, H.182 Ligands: 6ML.4 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.77 Metal complexes: A:C.18, A:C.21, A:C.121, A:C.159

1 x 6ML: oxygen-damaged SF4(Covalent)

6ML.4: 17 residues within 4Å: Chain A: G.17, C.18, T.19, G.20, C.21, E.77, G.78, G.119, T.120, C.121, G.158, C.159, P.160, P.161 Chain B: R.70, H.182 Ligands: SF4.3 11 PLIP interactions: 11 interactions with chain A, Hydrogen bonds: A:C.18, A:T.19, A:G.20, A:C.21, A:E.77, A:G.78 Water bridges: A:C.121 Metal complexes: A:C.18, A:C.21, A:C.121, A:C.159

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: S.42, E.44, H.60 Chain B: T.133, A.134, V.137, P.138 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:S.42, A:E.44, A:H.60, B:T.133, B:A.134 Water bridges: A:R.7 GOL.11: 10 residues within 4Å: Chain B: K.142, S.143, D.144, R.146, D.468, D.469, N.472, V.474, N.475, R.478 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.142, B:D.144, B:N.475 Water bridges: B:D.468, B:D.468, B:D.469, B:D.469

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

FCO.6: 13 residues within 4Å: Chain B: C.75, H.79, A.417, P.418, R.419, L.422, S.440, A.441, S.442, U.486, C.489 Ligands: NI.7, H2S.9 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.7: 7 residues within 4Å: Chain B: C.72, V.74, C.75, U.486, C.489 Ligands: FCO.6, H2S.9 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:C.75, B:C.489

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

FE2.8: 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.11, H2O.11, H2O.11

1 x H2S: HYDROSULFURIC ACID(Non-covalent)

H2S.9: 7 residues within 4Å: Chain B: C.72, V.74, C.75, R.419, U.486 Ligands: FCO.6, NI.7 No protein-ligand interaction detected (PLIP)

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

CL.10: 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

Zacarias, S. et al., A Hydrophilic Channel Is Involved in Oxidative Inactivation of a [NiFeSe] Hydrogenase. Acs Catalysis (2019)

Release Date

2019-09-04

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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