SMTL ID : 6gan.1

Structure of fully reduced Hydrogenase (Hyd-2) variant E14Q

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.192, C.195, R.197, R.198, F.201, C.220, L.221, Y.222, C.226, G.228, P.229, V.249 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.192, A:C.195, A:C.220, A:C.226 SF4.3: 13 residues within 4Å: Chain A: E.21, C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 Chain B: R.59, H.214 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.81 Metal complexes: A:C.22, A:C.25, A:C.120, A:C.154 SF4.7: 12 residues within 4Å: Chain C: H.192, C.195, R.197, R.198, F.201, C.220, L.221, Y.222, C.226, G.228, P.229, V.249 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.192, C:C.195, C:C.220, C:C.226 SF4.9: 13 residues within 4Å: Chain C: E.21, C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 Chain D: R.59, H.214 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.81 Metal complexes: C:C.22, C:C.25, C:C.120, C:C.154

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

F3S.2: 13 residues within 4Å: Chain A: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 Chain B: K.211, Q.216 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.235, A:C.255, A:C.258 F3S.8: 13 residues within 4Å: Chain C: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 Chain D: K.211, Q.216 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.235, C:C.255, C:C.258

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

FCO.4: 13 residues within 4Å: Chain B: C.64, T.67, H.68, A.477, P.478, R.479, L.482, V.500, P.501, S.502, C.546, C.549 Ligands: NI.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.479, B:R.479, B:S.502 Metal complexes: B:C.64, B:C.549 FCO.10: 13 residues within 4Å: Chain D: C.64, T.67, H.68, A.477, P.478, R.479, L.482, V.500, P.501, S.502, C.546, C.549 Ligands: NI.11 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.479, D:R.479, D:S.502 Metal complexes: D:C.64, D:C.549

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

NI.5: 5 residues within 4Å: Chain B: C.61, C.64, C.546, C.549 Ligands: FCO.4 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:C.64, B:C.546, B:C.549 NI.11: 5 residues within 4Å: Chain D: C.61, C.64, C.546, C.549 Ligands: FCO.10 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.61, D:C.64, D:C.546, D:C.549

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain B: E.42, Q.497, A.498, H.552 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.42, B:A.498, B:H.552, H2O.8, H2O.9, H2O.11 MG.12: 4 residues within 4Å: Chain D: E.42, Q.497, A.498, H.552 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.42, D:A.498, D:H.552, H2O.29, H2O.30, H2O.31

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, R.M. et al., Mechanistic Exploitation of a Self-Repairing, Blocked Proton Transfer Pathway in an O2-Tolerant [NiFe]-Hydrogenase. J. Am. Chem. Soc. (2018)

Release Date

2019-02-20

Peptides

Hydrogenase-2 small chain: AC
Hydrogenase-2 large chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

C
T

B
L

D
M

Hydrogenase-2 small chain

Hydrogenase-2 large chain

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