SMTL ID : 4ueq.2 (5 other biounits)

Structure of the V74C large subunit mutant of D. fructosovorans NiFe- hydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-mer

Ligands

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

SF4.1: 12 residues within 4Å: Chain A: H.184, C.187, R.189, L.190, F.193, C.212, L.213, Y.214, C.218, G.220, P.221, V.239 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.184, A:C.187, A:C.212, A:C.218 SF4.3: 12 residues within 4Å: Chain A: E.16, C.17, G.19, C.20, G.112, T.113, C.114, G.146, C.147, P.148 Chain B: R.84, H.242 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.147

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

F3S.2: 12 residues within 4Å: Chain A: T.223, N.225, C.227, F.232, W.237, P.238, C.245, L.246, G.247, C.248 Chain B: K.239, Q.244 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.227, A:C.245, A:C.248

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

FCO.4: 14 residues within 4Å: Chain B: C.89, V.92, H.93, A.488, P.489, R.490, L.493, V.511, P.512, S.513, C.557, C.560 Ligands: NI.5, H2S.6 8 PLIP interactions: 6 interactions with chain B, 2 Ligand-Water interactions Hydrogen bonds: B:R.490, B:R.490, B:S.513 Water bridges: B:C.89 Metal complexes: B:C.89, B:C.560, H2O.14, H2O.15

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

NI.5: 6 residues within 4Å: Chain B: C.86, C.89, C.557, C.560 Ligands: FCO.4, H2S.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.86, B:C.89, B:C.560, H2O.14, H2O.15

1 x H2S: HYDROSULFURIC ACID(Covalent)

H2S.6: 7 residues within 4Å: Chain B: C.86, C.89, R.490, C.557, C.560 Ligands: FCO.4, NI.5 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain B: E.67, L.509, H.563 Ligands: CA.8 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.67, B:L.509, B:H.563, H2O.14, H2O.14, H2O.23 MG.9: 1 residues within 4Å: Chain B: N.195 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 4 residues within 4Å: Chain B: E.67, L.509, H.563 Ligands: MG.7 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.67, B:L.509, B:H.563, H2O.14, H2O.14, H2O.23

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 8 residues within 4Å: Chain B: R.114, N.118, F.309, A.310, T.311, Q.324, W.456, E.459 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.114, B:R.114, B:N.118, B:F.309, B:E.459 GOL.11: 6 residues within 4Å: Chain A: A.55 Chain B: N.195, A.196, Y.197, L.199, R.543 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.195, B:L.199, B:R.543

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., [NiFe]-hydrogenases revisited: nickel-carboxamido bond formation in a variant with accrued O2-tolerance and a tentative re-interpretation of Ni-SI states. Metallomics (2015)

Release Date

2015-03-25

Peptides

HYDROGENASE (NIFE) SMALL SUBUNIT HYDA: A
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Q

HYDROGENASE (NIFE) SMALL SUBUNIT HYDA

NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT

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