SMTL ID : 9erc.1

Hydrogenase-2 Ni-Li state

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.31 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.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: 13 residues within 4Å: Chain A: E.20, C.21, G.23, C.24, 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 SF4.19: 12 residues within 4Å: Chain C: 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 SF4.21: 13 residues within 4Å: Chain C: E.20, C.21, G.23, C.24, G.117, S.118, C.119, V.125, G.152, C.153, P.154 Chain D: R.59, H.214 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.80 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.20: 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

15 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: K.207, E.208, F.209, L.223, H.269 Chain B: F.458, K.460 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.208, A:F.209, B:K.460, B:K.460 Water bridges: A:K.207, A:H.222, A:H.222, A:L.223, B:R.51, B:R.51 GOL.5: 2 residues within 4Å: Chain A: H.265, Q.270 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.265, A:Q.270 GOL.6: 4 residues within 4Å: Chain A: R.188, E.192 Chain C: R.204, W.218 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:W.218, A:R.188 Water bridges: C:R.204, C:E.216, A:L.189, A:E.192 GOL.8: 7 residues within 4Å: Chain A: G.267, I.268, H.269, Q.270 Chain B: D.49, R.51, D.52 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.269, A:H.269 Water bridges: A:G.267 GOL.12: 5 residues within 4Å: Chain B: M.241, Y.443, I.447 Chain C: A.165, T.169 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.443 GOL.13: 3 residues within 4Å: Chain B: A.267, F.268, L.408 1 PLIP interactions: 1 interactions with chain B Water bridges: B:L.408 GOL.14: 7 residues within 4Å: Chain B: E.77, S.78, N.81, I.82, D.83, N.294, S.319 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.82, B:D.83, B:N.294, B:S.319, B:S.319 Water bridges: B:N.81 GOL.18: 5 residues within 4Å: Chain A: H.199, R.204, W.218 Chain C: R.188, E.192 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.188, A:W.218 Water bridges: C:G.187 GOL.22: 7 residues within 4Å: Chain C: K.207, E.208, F.209, L.223, H.269 Chain D: F.458, K.460 10 PLIP interactions: 4 interactions with chain D, 6 interactions with chain C Hydrogen bonds: D:K.460, D:K.460, C:E.208, C:F.209 Water bridges: D:R.51, D:R.51, C:K.207, C:H.222, C:H.222, C:L.223 GOL.23: 7 residues within 4Å: Chain C: G.267, I.268, H.269, Q.270 Chain D: D.49, R.51, D.52 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:H.269 Water bridges: D:D.49 GOL.27: 3 residues within 4Å: Chain D: A.267, F.268, L.408 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.408 GOL.28: 5 residues within 4Å: Chain D: R.51, K.460, P.461, N.462, I.463 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.460, D:K.460, D:I.463, D:I.463 Water bridges: D:R.51 GOL.29: 8 residues within 4Å: Chain D: E.42, E.43, K.46, G.347, T.348, N.495, Y.496, Q.497 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.349, D:Y.496, D:Y.496, D:Q.497 Water bridges: D:K.46 GOL.30: 5 residues within 4Å: Chain A: A.165, T.169 Chain D: M.241, Y.443, I.447 No protein-ligand interaction detected (PLIP) GOL.31: 8 residues within 4Å: Chain B: R.203, F.246 Chain D: E.196, R.203, F.246, K.249 Ligands: MG.17, MG.33 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:R.203 Water bridges: B:K.249, B:K.249, B:K.249, B:K.249, B:K.249, D:K.249, D:K.249

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

MG.7: 1 residues within 4Å: Chain A: D.87 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.87, H2O.6 MG.11: 3 residues within 4Å: Chain B: E.42, 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.10, H2O.12, H2O.12 MG.15: 5 residues within 4Å: Chain B: K.178, Y.269, P.270, E.271, W.272 No protein-ligand interaction detected (PLIP) MG.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain B: E.196 Ligands: GOL.31 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.196, H2O.12, H2O.12, H2O.24 MG.26: 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.37, H2O.37, H2O.37 MG.32: 2 residues within 4Å: Chain D: N.228, L.229 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain D: E.196 Ligands: GOL.31 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.196, H2O.36, H2O.37, H2O.49

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

FCO.9: 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.10 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.24: 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.25 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.10: 5 residues within 4Å: Chain B: C.61, C.64, C.546, C.549 Ligands: FCO.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.61, B:C.64, B:C.546, B:C.549 NI.25: 5 residues within 4Å: Chain D: C.61, C.64, C.546, C.549 Ligands: FCO.24 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.61, D:C.64, D:C.546, D:C.549

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

2025-04-02

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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