SMTL ID : 5d08.1 (1 other biounit)

Crystal structure of selenomethionine-labeled epoxyqueuosine reductase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

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

SF4.1: 10 residues within 4Å: Chain A: A.181, K.182, N.183, C.216, C.219, K.221, C.222, C.275, P.276, L.277 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.216, A:C.219, A:C.222, A:C.275 SF4.2: 11 residues within 4Å: Chain A: C.226, P.227, T.228, L.231, L.237, C.242, I.243, C.268, T.270, C.271 Ligands: B12.3 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.226, A:C.242, A:C.268, A:C.271

1 x B12: COBALAMIN(Non-covalent)

B12.3: 39 residues within 4Å: Chain A: S.60, L.61, R.64, S.75, F.77, E.78, R.85, C.125, Y.133, D.162, G.164, L.166, S.167, D.168, R.169, A.170, E.173, S.180, N.183, C.184, M.185, I.186, S.193, V.195, Y.196, L.197, P.234, G.235, L.237, C.242, S.244, F.245, G.267, C.268, D.269, C.271, Q.272 Ligands: SF4.2, GOL.4 31 PLIP interactions: 30 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:F.77, A:F.77, A:D.168, A:L.197, A:L.237 Hydrogen bonds: A:R.85, A:R.85, A:D.162, A:D.162, A:S.167, A:D.168, A:R.169, A:R.169, A:S.180, A:N.183, A:I.186, A:I.186, A:L.197, A:L.197, A:C.268, A:D.269 Water bridges: A:E.78, A:E.78, A:E.79, A:G.164, A:R.169, A:V.195, A:Q.272 Salt bridges: A:R.169 pi-Cation interactions: A:R.64 Metal complexes: H2O.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: F.77, D.162, Q.248, Y.266, W.322 Ligands: B12.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.133, A:D.162, A:Q.248, A:Q.248, A:Y.266 Water bridges: A:H.134, A:D.162

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 6 residues within 4Å: Chain A: V.136, K.140, L.285, H.286, P.287, E.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.285, A:E.288 Salt bridges: A:K.140, A:H.286 PO4.6: 2 residues within 4Å: Chain A: K.382, K.386 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.386 Salt bridges: A:K.382, A:K.386

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

CL.7: 1 residues within 4Å: Chain A: E.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dowling, D.P. et al., Molecular basis of cobalamin-dependent RNA modification. Nucleic Acids Res. (2016)

Release Date

2016-09-28

Peptides

Epoxyqueuosine reductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Epoxyqueuosine reductase

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