SMTL ID : 6w13.1

Human 8-oxoguanine glycosylase interrogating fully intrahelical oxoG lesion DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 Å

Oligo State

monomer

Ligands

1 x DC- DA- 8OG- DG- DT- DC- DT: DNA (5'-D(P*CP*AP*(8OG)P*GP*TP*CP*T)-3')(Non-covalent)

DC-DA-8OG-DG-DT-DC-DT.1: 18 residues within 4Å: Chain A: N.141, P.236, G.237, V.238, G.239, T.240, K.241, V.242, D.260, V.261 Ligands: DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2, MG.4, S5Y.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.141, A:N.141

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

DA-DC-DC-DT-DG-DG.2: 12 residues within 4Å: Chain A: N.141, N.143, R.146, Y.195, R.196 Ligands: DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, S5Y.9 Protein-ligand interaction information (PLIP) not available

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 6 residues within 4Å: Chain A: Q.35, S.36, Q.127, C.132, S.135, F.136 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:Q.35, H2O.3 MG.4: 4 residues within 4Å: Chain A: C.233, L.235, V.238 Ligands: DC-DA-8OG-DG-DT-DC-DT.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.233, A:L.235, A:V.238, H2O.2 MG.5: 6 residues within 4Å: Chain A: H.104, W.105, W.299, G.300, P.301, Y.302 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:W.299 MG.6: 6 residues within 4Å: Chain A: L.179, A.180, G.181, V.184, S.201, R.205 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:L.179, A:G.181, A:S.201

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 3 residues within 4Å: Chain A: Y.225, H.229, D.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.225 Water bridges: A:R.296 Salt bridges: A:H.229, A:K.289, A:R.296 ACT.8: 6 residues within 4Å: Chain A: V.50, L.51, A.52, Y.91, D.128, E.131 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.91 Hydrogen bonds: A:A.52, A:D.128

1 x S5Y: 2-(2-ethoxyethoxy)ethanethiol(Non-covalent)

S5Y.9: 8 residues within 4Å: Chain A: Y.195, R.198, C.199 Ligands: DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DC-DA-8OG-DG-DT-DC-DT.1, DA-DC-DC-DT-DG-DG.2, DA-DC-DC-DT-DG-DG.2 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shigdel, U.K. et al., The trajectory of intrahelical lesion recognition and extrusion by the human 8-oxoguanine DNA glycosylase. Nat Commun (2020)

Release Date

2020-09-23

Peptides

N-glycosylase/DNA lyase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-glycosylase/DNA lyase