SMTL ID : 5xvd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.42, 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.2, H2O.2, H2O.4 MG.11: 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.26, H2O.26, H2O.28

2 x NFV: NI-FE OXIDIZED ACTIVE CENTER(Non-covalent)

NFV.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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.479, A:R.479, A:S.502 Metal complexes: A:C.61, A:C.64, A:C.64, A:C.549, A:C.549 NFV.12: 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 9 PLIP interactions: 9 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.549, C:C.549

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.74, E.77, S.78, V.84, N.294, H.318, V.472 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:E.77, A:S.78, A:S.319, A:V.472 Water bridges: A:S.78, A:N.294, A:H.318, A:H.318, A:H.318, A:S.319 GOL.4: 7 residues within 4Å: Chain A: A.176, Q.178, E.271, W.272, R.275, R.538 Ligands: NA.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.176, A:E.271, A:R.275, A:R.275, A:R.538 GOL.10: 7 residues within 4Å: Chain A: F.458, K.460 Chain B: K.208, E.209, F.210, L.224, H.270 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.209, B:F.210, A:R.51 Water bridges: B:K.208, B:H.223, B:H.223, B:L.224 GOL.18: 7 residues within 4Å: Chain C: F.458, K.460 Chain D: K.208, E.209, F.210, L.224, H.270 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.209, D:F.210, C:R.51 Water bridges: D:K.208, D:H.223, D:H.223, D:L.224

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 6 residues within 4Å: Chain A: Q.178, Y.269, P.270, E.271, W.272 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.178, A:Q.178, A:E.271 NA.13: 5 residues within 4Å: Chain C: Q.178, Y.269, P.270, E.271, W.272 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.178, C:Y.269, C:E.271 Water bridges: C:R.275

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

SF4.6: 11 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, V.249 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:H.192, B:C.195, B:C.220, B:C.226 SF4.8: 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, G.153, C.154, P.155 Ligands: 8JU.9 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Ligand interactions Metal complexes: B:C.22, B:C.25, B:C.120, B:C.154, 8JU.9, 8JU.9 SF4.14: 12 residues within 4Å: Chain D: H.192, C.195, R.197, R.198, F.201, C.220, L.221, Y.222, C.226, G.228, P.229, V.249 4 PLIP interactions: 4 interactions with chain D, Metal complexes: D:H.192, D:C.195, D:C.220, D:C.226 SF4.16: 12 residues within 4Å: Chain C: H.214 Chain D: E.21, C.22, G.24, C.25, G.118, S.119, C.120, G.153, C.154, P.155 Ligands: 8JU.17 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Ligand interactions Metal complexes: D:C.22, D:C.25, D:C.120, D:C.154, 8JU.17, 8JU.17

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

F3S.7: 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.15: 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

2 x 8JU: FE4-S4-O CLUSTER(Non-covalent)

8JU.9: 16 residues within 4Å: Chain A: R.59, H.214 Chain B: E.21, C.22, T.23, G.24, C.25, D.81, G.82, G.118, S.119, C.120, G.153, C.154, P.155 Ligands: SF4.8 5 PLIP interactions: 5 interactions with chain B, Hydrogen bonds: B:G.82 Metal complexes: B:C.22, B:C.25, B:C.120, B:C.154 8JU.17: 16 residues within 4Å: Chain C: R.59, H.214 Chain D: E.21, C.22, T.23, G.24, C.25, D.81, G.82, G.118, S.119, C.120, G.153, C.154, P.155 Ligands: SF4.16 6 PLIP interactions: 6 interactions with chain D, Hydrogen bonds: D:G.82 Water bridges: D:C.120 Metal complexes: D:C.22, D:C.25, D:C.120, D:C.154

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
Hydrogenase-2 small chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

C
M

B
S

D
T

[NiFe]-hydrogenase 2 large subunit

Hydrogenase-2 small chain

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