SMTL ID : 8dw4.1

Glycosylase MutY variant N146S in complex with DNA containing d(8-oxo-G) paired with an abasic site product (AP) generated by the enzyme in crystals by removal of calcium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.49 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, L.193, V.197, C.198, P.203, 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 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.346, A:R.350 Hydrogen bonds: A:Q.349 Salt bridges: A:R.353

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

NA.3: 4 residues within 4Å: Chain A: S.118, L.120, V.123 Chain C: C.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Demir, M. et al., Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism. Nucleic Acids Res. (2023)

Release Date

2022-11-30

Peptides

Adenine DNA glycosylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Adenine DNA glycosylase

Related Entries With Identical Sequence