SMTL ID : 8dwd.1

Adenine glycosylase MutY variant E43S in complex with DNA containing d(8-oxo-G) paired with an AP site generated by the enzyme acting on purine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

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

SF4.1: 14 residues within 4Å: Chain A: R.153, L.154, V.197, C.198, P.203, S.204, C.205, C.208, V.210, Q.211, C.214, A.216, F.217, A.222 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.198, A:C.205, A:C.208, A:C.214

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: V.346, Q.349, R.350, R.353 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.346, A:Q.349, A:R.350 Hydrogen bonds: A:Q.349 Water bridges: A:R.350 Salt bridges: A:R.353

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: S.118, V.123, G.124 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:S.118, A:V.123, H2O.1, H2O.5, H2O.8 CA.4: 3 residues within 4Å: Chain A: D.257, T.259, G.260 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.259, A:T.259, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Russelburg, L.P. et al., Structural Basis for Base Engagement and Stereochemistry Revealed by Alteration of Catalytic Residue Glu43 in DNA Repair Glycosylase MutY. To Be Published

Release Date

2023-08-09

Peptides

Adenine DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenine DNA glycosylase

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