SMTL ID : 8xxg.1

Crystal structure of human 8-oxoguanine glycosylase K249H mutant bound to the reaction intermediate derived from the crystal soaked into the solution at pH 4.0 under 277 K for 2.5 hours

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

monomer

Ligands

1 x DA- DG- DC- DG- DT- DC- DC- DA: DNA (5'-D(*AP*GP*CP*GP*TP*CP*CP*A)-3')(Non-covalent)

DA-DG-DC-DG-DT-DC-DC-DA.1: 15 residues within 4Å: Chain A: C.9, T.10, G.11, G.12, A.13, C.14, G.15, C.16 Chain B: N.140, N.141, N.142, V.260, H.264 Ligands: DG-DT-DC-DT-DA-DC-DC.2, 01.3 Protein-ligand interaction information (PLIP) not available

1 x DG- DT- DC- DT- DA- DC- DC: DNA (5'-D(P*GP*TP*CP*TP*AP*CP*C)-3')(Non-covalent)

DG-DT-DC-DT-DA-DC-DC.2: 25 residues within 4Å: Chain A: G.2, G.3, T.4, A.5, G.6, A.7, C.8 Chain B: S.139, N.140, N.141, Y.194, Y.198, L.234, P.235, G.236, V.237, G.238, T.239, H.240, V.241, D.259, V.260 Ligands: DA-DG-DC-DG-DT-DC-DC-DA.1, 01.3, MG.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.194 Hydrogen bonds: B:N.140, B:N.140, B:R.145, B:R.145, B:R.188, B:Y.194, B:R.195, B:R.195 Water bridges: B:N.142, B:N.142, B:N.142, B:R.188, B:G.193, B:S.277, B:S.277, B:K.288

1 x 01: [(2~{R},3~{S},5~{S})-5-[2-azanyl-6,8-bis(oxidanylidene)-1,7-dihydropurin-9-yl]-2,3,5-tris(oxidanyl)pentyl] dihydrogen phosphate

01.3: 19 residues within 4Å: Chain B: G.33, F.36, F.135, S.138, N.141, N.142, I.143, I.146, H.240, M.248, P.257, D.259, H.261, M.262, Q.306, F.310, L.314 Ligands: DA-DG-DC-DG-DT-DC-DC-DA.1, DG-DT-DC-DT-DA-DC-DC.2 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:S.138, B:I.143, B:D.259, B:D.259, B:Q.306 Water bridges: B:A.144, B:Q.306 Salt bridges: B:D.259, B:H.261 pi-Stacking: B:F.310 pi-Cation interactions: B:F.310

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain B: C.232, I.233, L.234, V.237 Ligands: DG-DT-DC-DT-DA-DC-DC.2 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.232, B:L.234, B:V.237, H2O.13, H2O.16

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain B: Q.210, A.230, I.233 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.210, B:Q.210 Water bridges: B:W.215

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

N-glycosylase/DNA lyase

Related Entries With Identical Sequence