SMTL ID : 4upv.2 (1 other biounit)

Low X-ray dose structure of a Ni-A Ni-Sox mixture of the D. fructosovorans NiFe-hydrogenase L122A mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.52 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.185, C.188, R.190, L.191, F.194, C.213, L.214, Y.215, C.219, G.221, P.222, V.240 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.185, A:C.188, A:C.213, A:C.219 SF4.3: 12 residues within 4Å: Chain A: E.17, C.18, G.20, C.21, G.113, T.114, C.115, G.147, C.148, P.149 Chain B: R.84, H.242 5 PLIP interactions: 5 interactions with chain A, Salt bridges: A:E.76 Metal complexes: A:C.18, A:C.21, A:C.115, A:C.148

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

F3S.2: 12 residues within 4Å: Chain A: T.224, N.226, C.228, F.233, W.238, P.239, C.246, L.247, G.248, C.249 Chain B: K.239, Q.244 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.228, A:C.246, A:C.249

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: D.83, Q.86 Chain B: Y.373, T.374 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:T.374, A:D.83, A:Q.86 Water bridges: A:D.83 GOL.5: 5 residues within 4Å: Chain A: D.44, Q.63, A.64, G.67 Chain B: T.194 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:S.42, A:S.42, A:A.64, A:K.68, B:Q.189, B:G.191 Hydrogen bonds: B:T.194 GOL.6: 3 residues within 4Å: Chain A: F.194, F.199, Y.215 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.215 Water bridges: A:S.197 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:W.456

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

FCO.7: 13 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.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Hydrogen bonds: B:R.490, B:R.490, B:S.513 Metal complexes: B:C.560, H2O.11

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

NI.8: 5 residues within 4Å: Chain B: C.86, C.89, C.557, C.560 Ligands: FCO.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.86, B:C.560, H2O.11

1 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 3 residues within 4Å: Chain B: E.67, L.509, H.563 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.67, B:L.509, B:H.563, H2O.11, H2O.11, H2O.12

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.11: 3 residues within 4Å: Chain B: H.202, K.203, R.543 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Volbeda, A. et al., Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. J. Biol. Inorg. Chem. (2015)

Release Date

2014-10-29

Peptides

NIFE-HYDROGENASE SMALL SUBUNIT: A
NIFE-HYDROGENASE LARGE SUBUNIT: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
Q

NIFE-HYDROGENASE SMALL SUBUNIT

NIFE-HYDROGENASE LARGE SUBUNIT

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