SMTL ID : 5y4n.1

Crystal structure of aerobically purified and anaerobically crystallized D. vulgaris Miyazaki F [NiFe]-hydrogenase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 13 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, E.75, G.112, T.113, C.114, G.149, C.150, P.151 Chain B: R.79, H.235 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.75 Metal complexes: A:C.17, A:C.20, A:C.114, A:C.150 SF4.2: 12 residues within 4Å: Chain A: H.188, C.191, R.193, L.194, F.197, C.216, L.217, Y.218, C.222, G.224, P.225, V.243 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.188, A:C.191, A:C.216, A:C.222

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

F3S.3: 12 residues within 4Å: Chain A: T.227, N.229, C.231, F.236, W.241, P.242, C.249, I.250, G.251, C.252 Chain B: K.232, Q.237 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.231, A:C.249, A:C.252

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 2 residues within 4Å: Chain A: L.194, D.198 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.198, A:D.198

3 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 8 residues within 4Å: Chain A: R.193, A.211, R.212, K.213, G.214, D.244 Chain B: Y.247, D.248 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.247 Water bridges: B:R.254, A:R.193, A:D.244 Hydrogen bonds: A:R.212, A:D.244 MRD.9: 5 residues within 4Å: Chain A: A.82, Y.86 Chain B: P.359, K.360, Y.361 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.82 Hydrogen bonds: A:Y.86, A:Y.86, B:Y.361 MRD.10: 1 residues within 4Å: Chain B: E.348 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.348 Water bridges: B:E.348, B:E.348

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.6: 6 residues within 4Å: Chain A: T.116, F.117, N.134, N.146, L.176, N.177 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.134, A:N.146 Water bridges: A:N.134, A:N.134, A:D.135

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 3 residues within 4Å: Chain B: E.62, L.498, H.552 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.62, B:L.498, B:H.552, H2O.14, H2O.14, H2O.15

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

NFU.8: 13 residues within 4Å: Chain B: C.81, C.84, T.87, H.88, 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 B Hydrogen bonds: B:T.87, B:R.479, B:R.479, B:S.502 Metal complexes: B:C.81, B:C.84, B:C.84, B:C.549, B:C.549

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nishikawa, K. et al., Ni-elimination from the active site of the standard [NiFe]‐hydrogenase upon oxidation by O2. J.Inorg.Biochem. (2017)

Release Date

2018-08-08

Peptides

Periplasmic [NiFe] hydrogenase small subunit: A
Periplasmic [NiFe] hydrogenase large subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
S

B
L

Periplasmic [NiFe] hydrogenase small subunit

Periplasmic [NiFe] hydrogenase large subunit

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