SMTL ID : 6g7m.1

Four-site variant (Y222C, C197S, C432S, C433S) of E. coli hydrogenase-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

hetero-2-2-mer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: H.192, C.195, R.197, R.198, C.220, L.221, C.222, C.226, G.228, V.249 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.192, A:C.195, A:C.220, A:C.226 SF4.3: 12 residues within 4Å: Chain A: C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 Chain B: R.59, H.214 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:D.81 Metal complexes: A:C.22, A:C.25, A:C.120, A:C.154 SF4.8: 11 residues within 4Å: Chain C: H.192, C.195, R.197, R.198, C.220, L.221, C.222, C.226, G.228, P.229, V.249 4 PLIP interactions: 4 interactions with chain C, Metal complexes: C:H.192, C:C.195, C:C.220, C:C.226 SF4.10: 13 residues within 4Å: Chain C: E.21, C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 Chain D: R.59, H.214 6 PLIP interactions: 5 interactions with chain C, 1 Ligand-Water interactions Salt bridges: C:D.81 Metal complexes: C:C.22, C:C.25, C:C.120, C:C.154, H2O.24

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

F3S.2: 13 residues within 4Å: Chain A: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 Chain B: K.211, Q.216 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.235, A:C.255, A:C.258 F3S.9: 13 residues within 4Å: Chain C: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 Chain D: K.211, Q.216 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.235, C:C.255, C:C.258

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

FCO.4: 12 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.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.18 FCO.11: 12 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.549 Ligands: NI.12 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.35

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 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.61, B:C.64, B:C.546, B:C.549, H2O.18 NI.12: 5 residues within 4Å: Chain D: C.61, C.64, C.546, C.549 Ligands: FCO.11 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.61, D:C.64, D:C.546, D:C.549, H2O.35

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.7, H2O.8, H2O.8 MG.7: 1 residues within 4Å: Chain B: N.81 No protein-ligand interaction detected (PLIP) MG.13: 3 residues within 4Å: Chain D: E.42, 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.25, H2O.26, H2O.26 MG.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, L. et al., Direct visible light activation of a surface cysteine-engineered [NiFe]-hydrogenase by silver nanoclusters. Energy Environ Sci (2019)

Release Date

2019-04-03

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