SMTL ID : 8xwc.1

Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the substrate 8-oxoguanine DNA at pH 8.0 under 277 K

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 2 residues within 4Å: Chain B: G.14, C.15 No protein-ligand interaction detected (PLIP)

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: C.12, T.13 Chain B: G.5, A.6, C.7 No protein-ligand interaction detected (PLIP) GOL.3: 6 residues within 4Å: Chain C: Y.224, H.228, T.239, D.243, K.288, R.295 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:T.239, C:T.239, C:R.295 Water bridges: C:Y.224, C:E.225, C:H.228 GOL.4: 3 residues within 4Å: Chain C: Q.267, R.268, S.271 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.267, C:R.268 Water bridges: C:S.271

1 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 5 residues within 4Å: Chain A: C.12 Chain C: C.232, I.233, L.234, V.237 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:C.232, C:L.234, C:V.237, H2O.1, H2O.13

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

NA.6: 3 residues within 4Å: Chain C: A.214, W.215, Q.218 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.218 Water bridges: C:Q.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Unno, M. et al., Capturing a glycosylase reaction intermediate in DNA repair by freeze-trapping of a pH-responsive hOGG1 mutant. Nucleic Acids Res. (2025)

Release Date

2025-07-23

Peptides

N-glycosylase/DNA lyase: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

N-glycosylase/DNA lyase

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