SMTL ID : 5t8y.2 (1 other biounit)

Structure of epoxyqueuosine reductase from Bacillus subtilis with the Asp134 catalytic loop swung out of the active site.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

monomer

Ligands

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

SF4.1: 9 residues within 4Å: Chain A: A.181, K.182, N.183, C.216, C.219, K.221, C.222, C.275, P.276 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.216, A:C.219, A:C.222, A:C.275 SF4.2: 10 residues within 4Å: Chain A: C.226, P.227, 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: 40 residues within 4Å: Chain A: S.60, L.61, R.64, L.65, S.75, F.77, E.78, R.85, C.125, A.127, Y.133, 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, Q.248, G.267, C.268, D.269, C.271, Q.272 Ligands: SF4.2, PO4.8 24 PLIP interactions: 24 interactions with chain A, Hydrophobic interactions: A:L.65, A:F.77, A:E.78, A:D.168 Hydrogen bonds: A:R.85, A:R.85, A:L.166, A:S.167, A:D.168, 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:S.244, A:C.268, A:D.269 Water bridges: A:R.169 Salt bridges: A:R.169 pi-Cation interactions: A:R.64

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

PO4.4: 1 residues within 4Å: Chain A: K.382 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.382 PO4.5: 1 residues within 4Å: Ligands: PO4.6 No protein-ligand interaction detected (PLIP) PO4.6: 3 residues within 4Å: Chain A: T.273 Ligands: PO4.5, PO4.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.273 PO4.7: 3 residues within 4Å: Chain A: T.270, T.273 Ligands: PO4.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.270, A:T.273 PO4.8: 5 residues within 4Å: Chain A: H.134, M.160, G.164, D.168 Ligands: B12.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.164, A:G.164 Salt bridges: A:H.134

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
B

Epoxyqueuosine reductase

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