SMTL ID : 4uew.3 (2 other biounits)

Structure of H2-treated anaerobically purified D. fructosovorans NiFe- hydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.08 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.70, H.228 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.225, Q.230 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.227, A:C.245, A:C.248

7 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.168, L.169, K.176 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.169, A:K.176 Water bridges: A:P.167, A:K.176, A:K.176 GOL.5: 5 residues within 4Å: Chain A: K.140, L.169, D.170, E.171 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.140, A:K.140 Water bridges: A:L.169 GOL.6: 6 residues within 4Å: Chain A: K.4, R.6, L.37 Chain B: A.169, F.170, S.173 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.6, A:D.38 Water bridges: A:R.6, B:F.170 GOL.10: 9 residues within 4Å: Chain B: R.100, M.101, N.104, F.295, A.296, T.297, Q.310, W.442, E.445 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.100, B:R.100, B:N.104, B:F.295, B:E.445 Water bridges: B:Q.310 GOL.11: 6 residues within 4Å: Chain A: A.55 Chain B: N.181, A.182, Y.183, L.185, R.529 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.181, B:L.185, B:R.529 GOL.12: 8 residues within 4Å: Chain B: G.281, G.282, I.283, G.284, G.285, R.319, T.416, H.419 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.281, B:I.283, B:G.285, B:R.319, B:R.319 GOL.13: 3 residues within 4Å: Chain B: K.337, Y.338, D.366 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.337, B:D.366, B:D.366

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

FCO.7: 13 residues within 4Å: Chain B: C.75, V.78, H.79, A.474, P.475, R.476, L.479, V.497, P.498, S.499, C.543, C.546 Ligands: NI.8 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.476, B:R.476, B:S.499 Metal complexes: B:C.75, B:C.546

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

NI.8: 5 residues within 4Å: Chain B: C.72, C.75, C.543, C.546 Ligands: FCO.7 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.72, B:C.75, B:C.546

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: E.53, L.495, H.549 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.53, B:L.495, B:H.549, H2O.14, H2O.14, H2O.23

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

PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT: A
PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Q

PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT

PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT

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