SMTL ID : 6ehs.1

E. coli Hydrogenase-2 chemically reduced structure

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 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.193, C.196, R.198, R.199, F.202, C.221, L.222, Y.223, C.227, G.229, P.230, V.250 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.193, A:C.196, A:C.221, A:C.227 SF4.3: 13 residues within 4Å: Chain A: E.22, C.23, G.25, C.26, G.119, S.120, C.121, V.127, G.154, C.155, P.156 Chain B: R.59, H.214 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.82 Metal complexes: A:C.23, A:C.26, A:C.121, A:C.155 SF4.9: 11 residues within 4Å: Chain C: H.193, C.196, R.198, R.199, C.221, L.222, Y.223, C.227, G.229, P.230, V.250 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.193, C:C.196, C:C.221, C:C.227 SF4.11: 13 residues within 4Å: Chain C: E.22, C.23, G.25, C.26, G.119, S.120, C.121, V.127, G.154, C.155, P.156 Chain D: R.59, H.214 5 PLIP interactions: 5 interactions with chain C, Salt bridges: C:D.82 Metal complexes: C:C.23, C:C.26, C:C.121, C:C.155

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

F3S.2: 13 residues within 4Å: Chain A: I.192, T.232, C.236, F.241, W.248, P.249, C.256, Y.257, G.258, C.259, N.260 Chain B: K.211, Q.216 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.236, A:C.256, A:C.259 F3S.10: 13 residues within 4Å: Chain C: I.192, T.232, C.236, F.241, W.248, P.249, C.256, Y.257, G.258, C.259, N.260 Chain D: K.211, Q.216 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.236, C:C.256, C:C.259

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 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.479, B:R.479, B:S.502 Metal complexes: B:C.64, B:C.549, H2O.19 FCO.12: 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.13 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Hydrogen bonds: D:R.479, D:R.479, D:S.502 Metal complexes: D:C.64, D:C.549, H2O.37

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: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.61, B:C.64, B:C.549, H2O.19 NI.13: 5 residues within 4Å: Chain D: C.61, C.64, C.546, C.549 Ligands: FCO.12 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.61, D:C.64, D:C.549, H2O.37

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 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.8, H2O.8, H2O.8 MG.14: 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.27, H2O.28, H2O.29

4 x DTN: DITHIONITE(Non-covalent)

DTN.7: 5 residues within 4Å: Chain A: T.34 Chain B: E.196, R.199, R.203 Chain D: K.249 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:E.196 DTN.8: 5 residues within 4Å: Chain B: L.298, R.391, D.437, I.438, N.441 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.437 DTN.15: 5 residues within 4Å: Chain B: K.249 Chain C: T.34 Chain D: E.196, R.199, R.203 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:E.196 DTN.16: 5 residues within 4Å: Chain D: L.298, R.391, D.437, I.438, N.441 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.298

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaton, S.E. et al., The structure of hydrogenase-2 fromEscherichia coli: implications for H2-driven proton pumping. Biochem. J. (2018)

Release Date

2018-04-18

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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