SMTL ID : 9erp.1

Hydrogenase-2 Ni-SI state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.37 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: I.190, H.191, C.194, R.196, R.197, F.200, C.219, L.220, Y.221, C.225, G.227, P.228, V.248 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.191, A:C.194, A:C.219, A:C.225 SF4.3: 16 residues within 4Å: Chain A: E.20, C.21, T.22, G.23, C.24, D.80, G.81, G.117, S.118, C.119, V.125, G.152, C.153, P.154 Chain B: R.59, H.214 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.21, A:C.24, A:C.119, A:C.153 SF4.9: 13 residues within 4Å: Chain C: I.190, H.191, C.194, R.196, R.197, F.200, C.219, L.220, Y.221, C.225, G.227, P.228, V.248 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.191, C:C.194, C:C.219, C:C.225 SF4.11: 16 residues within 4Å: Chain C: E.20, C.21, T.22, G.23, C.24, D.80, G.81, G.117, S.118, C.119, V.125, G.152, C.153, P.154 Chain D: R.59, H.214 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:C.21, C:C.24, C:C.119, C:C.153

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

F3S.2: 13 residues within 4Å: Chain A: I.190, T.230, C.234, F.239, W.246, P.247, C.254, Y.255, G.256, C.257, N.258 Chain B: K.211, Q.216 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.234, A:C.254, A:C.257 F3S.10: 13 residues within 4Å: Chain C: I.190, T.230, C.234, F.239, W.246, P.247, C.254, Y.255, G.256, C.257, N.258 Chain D: K.211, Q.216 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.234, C:C.254, C:C.257

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: K.207, E.208, F.209, H.222, L.223, H.269 Chain B: R.51, F.458, K.460 8 PLIP interactions: 2 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:R.51, B:K.460, A:E.208, A:E.208, A:E.208, A:F.209 Water bridges: A:H.222, A:L.223 GOL.12: 8 residues within 4Å: Chain C: K.207, E.208, F.209, L.223, H.269 Chain D: R.51, F.458, K.460 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:K.460, C:E.208, C:E.208, C:E.208, C:F.209 Water bridges: D:R.51, D:R.51 GOL.17: 7 residues within 4Å: Chain C: G.267, I.268, H.269, Q.270 Chain D: D.49, R.51, D.52 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:D.52, D:D.52, C:H.269 Water bridges: D:D.49, C:G.267

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

FCO.5: 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.6 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.13: 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.14 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.6: 6 residues within 4Å: Chain B: C.61, V.63, C.64, C.546, C.549 Ligands: FCO.5 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:C.64, B:C.546, B:C.549 NI.14: 6 residues within 4Å: Chain D: C.61, V.63, C.64, C.546, C.549 Ligands: FCO.13 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.61, D:C.64, D:C.546, D:C.549

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.7: 5 residues within 4Å: Chain B: E.42, K.366, 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.9, H2O.10, H2O.10 MG.8: 1 residues within 4Å: Chain B: S.311 No protein-ligand interaction detected (PLIP) MG.15: 5 residues within 4Å: Chain D: E.42, K.366, 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.35, H2O.36, H2O.36 MG.16: 2 residues within 4Å: Chain D: V.459, K.460 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carr, S.B. et al., Glutamate flick enables proton tunnelling during fast redox biocatalysis. To Be Published

Release Date

2025-04-09

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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