SMTL ID : 8dvy.1

DNA glycosylase MutY variant N146S in complex with DNA containing d(8-oxo-G) paired with an enzyme-generated abasic site product (AP) and crystalized with calcium acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

monomer

Ligands

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

SF4.1: 15 residues within 4Å: Chain A: V.150, 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 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.346, A:Q.349, A:R.350 Hydrogen bonds: A:Q.349 Salt bridges: A:R.353

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 3 residues within 4Å: Chain A: S.118, V.123, G.124 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.118, A:S.118, A:V.123, H2O.1, H2O.1 CA.4: 2 residues within 4Å: Chain A: D.257, T.259 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.257, A:T.259, A:T.259 CA.5: 4 residues within 4Å: Chain A: D.144, S.146 Chain C: A.6, X.7 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.144, A:S.146, H2O.1

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

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