SMTL ID : 5xvb.1

[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.42, Q.497, A.498, H.552 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.42, A:A.498, A:H.552, H2O.1, H2O.2, H2O.6 MG.8: 4 residues within 4Å: Chain C: E.42, Q.497, A.498, H.552 6 PLIP interactions: 3 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.42, C:A.498, C:H.552, H2O.12, H2O.13, H2O.14

2 x NFU: formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)(Non-covalent)

NFU.2: 13 residues within 4Å: Chain A: C.61, C.64, T.67, H.68, A.477, P.478, R.479, L.482, V.500, P.501, S.502, C.546, C.549 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:T.67, A:R.479, A:R.479, A:S.502 Metal complexes: A:C.61, A:C.64, A:C.64, A:C.546, A:C.549, A:C.549 NFU.9: 13 residues within 4Å: Chain C: C.61, C.64, T.67, H.68, A.477, P.478, R.479, L.482, V.500, P.501, S.502, C.546, C.549 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:T.67, C:R.479, C:R.479, C:S.502 Metal complexes: C:C.61, C:C.64, C:C.64, C:C.546, C:C.549, C:C.549

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: Q.178, E.271, W.272, R.275 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.275, A:R.275 Water bridges: A:Q.178, A:Q.178 GOL.4: 5 residues within 4Å: Chain A: M.241, Y.443, I.447 Chain D: A.166, T.170 No protein-ligand interaction detected (PLIP) GOL.10: 7 residues within 4Å: Chain C: A.176, Q.178, E.271, W.272, R.275, P.526, E.535 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.275 GOL.14: 8 residues within 4Å: Chain C: R.51, F.458, K.460 Chain D: K.208, E.209, F.210, L.224, H.270 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:F.210, D:H.223, C:R.51

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

SF4.5: 10 residues within 4Å: Chain B: H.192, C.195, R.197, R.198, C.220, L.221, Y.222, C.226, G.228, P.229 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.192, B:C.195, B:C.220, B:C.226 SF4.7: 13 residues within 4Å: Chain A: R.59, H.214 Chain B: E.21, C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.22, B:C.25, B:C.120, B:C.154 SF4.11: 10 residues within 4Å: Chain D: H.192, C.195, R.197, R.198, C.220, L.221, Y.222, C.226, G.228, P.229 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.192, D:C.195, D:C.220, D:C.226 SF4.13: 13 residues within 4Å: Chain C: R.59, H.214 Chain D: E.21, C.22, G.24, C.25, G.118, S.119, C.120, V.126, G.153, C.154, P.155 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:C.22, D:C.25, D:C.120, D:C.154

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

F3S.6: 13 residues within 4Å: Chain A: K.211, Q.216 Chain B: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.235, B:C.255, B:C.258 F3S.12: 13 residues within 4Å: Chain C: K.211, Q.216 Chain D: I.191, T.231, C.235, F.240, W.247, P.248, C.255, Y.256, G.257, C.258, N.259 3 PLIP interactions: 3 interactions with chain D, Metal complexes: D:C.235, D:C.255, D:C.258

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Noor, N.D.M. et al., Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2. Chem.Commun.(Camb.) (2018)

Release Date

2018-06-27

Peptides

[NiFe]-hydrogenase 2 large subunit: AC
[NiFe]-hydrogenase 2 small subunit: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
M

B
S

D
T

[NiFe]-hydrogenase 2 large subunit

[NiFe]-hydrogenase 2 small subunit

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