SMTL ID : 7nem.1

Hydrogenase-2 variant R479K - anaerobically oxidised form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 11 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, 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 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.80 Metal complexes: A:C.21, A:C.24, A:C.119, A:C.153 SF4.10: 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 SF4.12: 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.11: 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

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

FCO.4: 14 residues within 4Å: Chain B: C.64, T.67, H.68, A.477, P.478, K.479, L.482, V.500, P.501, S.502, C.546, C.549 Ligands: NI.5, OXY.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.479, B:S.502 Metal complexes: B:C.64, B:C.549 FCO.13: 14 residues within 4Å: Chain D: C.64, T.67, H.68, A.477, P.478, K.479, L.482, V.500, P.501, S.502, C.546, C.549 Ligands: NI.14, OXY.17 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:T.67, D:K.479, D:S.502 Metal complexes: D:C.64, D:C.549

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

NI.5: 6 residues within 4Å: Chain B: C.61, C.64, C.546, C.549 Ligands: FCO.4, OXY.9 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, C.64, C.546, C.549 Ligands: FCO.13, OXY.17 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.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.9, H2O.9, H2O.10 MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.15: 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.34, H2O.34, H2O.35 MG.16: 2 residues within 4Å: Chain D: N.81, N.294 No protein-ligand interaction detected (PLIP)

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 4 residues within 4Å: Chain A: R.215 Chain B: N.228, L.229, I.450 Ligand excluded by PLIP

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.9: 8 residues within 4Å: Chain B: C.61, V.63, C.64, K.479, C.546, C.549 Ligands: FCO.4, NI.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.64, B:K.479 Water bridges: B:K.479, B:K.479, B:K.479 OXY.17: 8 residues within 4Å: Chain D: C.61, V.63, C.64, K.479, C.546, C.549 Ligands: FCO.13, NI.14 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:C.64 Water bridges: D:K.479, D:K.479, D:K.479

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, R.M. et al., A comprehensive structural and kinetic investigation of the role of the active-site argininein bidirectional hydrogen activation by the [NiFe]-hydrogenase "Hyd-2) from Escherichia coli. To Be Published

Release Date

2022-03-02

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
T

C
S

B
M

D
L

Hydrogenase-2 small chain

Hydrogenase-2 large chain

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