SMTL ID : 8dwe.1 (1 other biounit)

Adenine glycosylase MutY variant E43Q in complex with DNA containing d(8-oxo-G) paired with substrate purine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

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

SF4.1: 13 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, 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 EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 2 residues within 4Å: Chain A: V.227, M.229 No protein-ligand interaction detected (PLIP)

2 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.2 CA.4: 2 residues within 4Å: Chain A: D.257, T.259 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.257, A:D.257, A:T.259, A:T.259, H2O.2

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 6 residues within 4Å: Chain B: G.8, G.9, A.10 Chain C: G.2, T.3, C.4 No protein-ligand interaction detected (PLIP)

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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