SMTL ID : 4ras.1 (4 other biounits)

Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

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

SF4.1: 11 residues within 4Å: Chain A: S.472, R.473, I.474, L.479, F.511, C.512, C.515, C.518, C.568, P.569, W.570 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.512, A:C.515, A:C.518, A:C.568 SF4.2: 10 residues within 4Å: Chain A: C.522, P.523, C.524, I.527, C.548, Y.551, C.561, R.563, C.564 Ligands: B12.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.522, A:C.548, A:C.561, A:C.564

1 x B12: COBALAMIN(Non-covalent)

B12.3: 37 residues within 4Å: Chain A: V.276, D.289, F.290, F.291, Y.379, Q.403, S.422, Y.426, S.455, V.457, I.458, H.459, N.460, P.461, I.463, V.471, I.474, D.476, T.477, L.478, S.487, K.488, S.489, F.535, Y.538, I.540, K.542, A.543, V.545, C.548, T.549, R.552, C.561, G.562, M.565 Ligands: SF4.2, CL.4 39 PLIP interactions: 39 interactions with chain A, Hydrophobic interactions: A:V.276, A:F.290, A:F.291, A:F.291, A:F.291, A:I.458, A:H.459, A:P.461, A:V.471, A:Y.538, A:V.545 Hydrogen bonds: A:F.290, A:Y.379, A:Q.403, A:S.422, A:S.455, A:V.457, A:H.459, A:H.459, A:I.474, A:D.476, A:D.476, A:T.477, A:L.478, A:L.478, A:K.488, A:S.489, A:S.489, A:K.542, A:K.542, A:C.561 Water bridges: A:S.487, A:Y.538, A:Y.538, A:C.561, A:Y.653, A:Q.658 Salt bridges: A:K.542 pi-Stacking: A:Y.538

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

CL.4: 4 residues within 4Å: Chain A: Y.426, K.488, R.552 Ligands: B12.3 Ligand excluded by PLIP

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

NA.5: 3 residues within 4Å: Chain A: K.566, C.568, N.571 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.571

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Payne, K.A. et al., Reductive dehalogenase structure suggests a mechanism for B12-dependent dehalogenation. Nature (2015)

Release Date

2014-10-15

Peptides

Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Oxidoreductase, NAD-binding/iron-sulfur cluster-binding protein

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