SMTL ID : 8dqv.1

The 1.52 angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - catalytic dimer (Huc2S2L)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-2-mer

Ligands

2 x O: OXYGEN ATOM(Non-covalent)

O.1: 8 residues within 4Å: Chain A: C.59, I.61, C.62, R.440, C.507, C.510 Ligands: FCO.3, 3NI.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.440 O.9: 7 residues within 4Å: Chain C: I.61, C.62, R.440, C.507, C.510 Ligands: FCO.11, 3NI.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.440

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 7 residues within 4Å: Chain A: E.40, E.300, K.338, Q.458, V.459, V.460, H.513 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.40, A:V.459, A:H.513, H2O.1, H2O.2, H2O.3 MG.10: 7 residues within 4Å: Chain C: E.40, E.300, K.338, Q.458, V.459, V.460, H.513 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.40, C:V.459, C:H.513, H2O.12, H2O.14, H2O.14

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

FCO.3: 13 residues within 4Å: Chain A: C.62, H.66, A.438, A.439, R.440, L.443, T.461, P.462, T.463, C.507, C.510 Ligands: O.1, 3NI.4 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.440, A:R.440, A:T.463, A:T.463 Metal complexes: A:C.62, A:C.510, O.1 FCO.11: 13 residues within 4Å: Chain C: C.62, H.66, A.438, A.439, R.440, L.443, T.461, P.462, T.463, C.507, C.510 Ligands: O.9, 3NI.12 7 PLIP interactions: 6 interactions with chain C, 1 Ligand-Ligand interactions Hydrogen bonds: C:R.440, C:R.440, C:T.463, C:T.463 Metal complexes: C:C.62, C:C.510, O.9

2 x 3NI: NICKEL (III) ION(Non-covalent)

3NI.4: 9 residues within 4Å: Chain A: C.59, I.61, C.62, R.440, C.507, V.509, C.510 Ligands: O.1, FCO.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:C.59, A:C.62, A:C.507, A:C.510, O.1 3NI.12: 9 residues within 4Å: Chain C: C.59, I.61, C.62, R.440, C.507, V.509, C.510 Ligands: O.9, FCO.11 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:C.59, C:C.62, C:C.507, C:C.510, O.9

2 x VK3: MENADIONE(Non-covalent)

VK3.5: 15 residues within 4Å: Chain B: F.207, F.208, K.211, Q.212, S.213, C.225, F.227, Y.228, M.286, I.287, P.288, Y.300, M.301, A.304, R.308 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.208, B:K.211, B:K.211, B:F.227, B:F.227, B:Y.228, B:Y.228 Hydrogen bonds: B:Y.300, B:R.308 Water bridges: B:S.213 pi-Stacking: B:Y.228 VK3.13: 15 residues within 4Å: Chain D: F.207, F.208, K.211, Q.212, S.213, C.225, F.227, Y.228, M.286, I.287, P.288, Y.300, M.301, A.304, R.308 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:F.208, D:K.211, D:K.211, D:F.227, D:F.227, D:Y.228, D:Y.228 Hydrogen bonds: D:Y.300, D:R.308 Water bridges: D:S.213 pi-Stacking: D:Y.228

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

F3S.6: 15 residues within 4Å: Chain A: R.57, H.163 Chain B: A.10, C.11, S.12, G.13, N.14, E.71, G.72, G.110, D.111, C.112, G.159, C.160, P.161 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.11, B:C.112, B:C.160 F3S.7: 14 residues within 4Å: Chain A: Q.160 Chain B: W.166, T.198, T.237, S.239, C.241, W.246, K.252, T.253, C.259, L.260, G.261, C.262, T.263 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.241, B:C.259, B:C.262 F3S.8: 13 residues within 4Å: Chain B: T.198, Q.199, C.202, R.204, V.205, F.208, C.225, L.226, F.227, C.232, G.234, P.235, T.253 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.202, B:C.225, B:C.232 F3S.14: 14 residues within 4Å: Chain C: Q.160 Chain D: W.166, T.198, T.237, S.239, C.241, W.246, K.252, T.253, C.259, L.260, G.261, C.262, T.263 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.241, D:C.259, D:C.262 F3S.15: 13 residues within 4Å: Chain D: T.198, Q.199, C.202, R.204, V.205, F.208, C.225, L.226, F.227, C.232, G.234, P.235, T.253 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.202, D:C.225, D:C.232 F3S.16: 15 residues within 4Å: Chain C: R.57, H.163 Chain D: A.10, C.11, S.12, G.13, N.14, E.71, G.72, G.110, D.111, C.112, G.159, C.160, P.161 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.11, D:C.112, D:C.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grinter, R. et al., Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature (2023)

Release Date

2023-01-04

Peptides

Hydrogenase-2, large subunit: AC
Hydrogenase-2, small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Hydrogenase-2, large subunit

Hydrogenase-2, small subunit

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