SMTL ID : 1yqk.1

Human 8-oxoguanine glycosylase crosslinked with guanine containing DNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

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

DC-DA-DG-DG-DT-DC-DT-DA-DC.1: 30 residues within 4Å: Chain A: G.1, G.2, T.3, A.4, G.5, A.6, C.7, C.8, T.9, G.10, G.11 Chain B: S.140, C.141, N.142, N.143, I.144, Y.195, Y.199, L.235, P.236, G.237, V.238, G.239, T.240, K.241, V.242, D.260, H.262, F.311 Ligands: CA.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.195, B:R.196, B:R.196, B:S.284, B:S.284 Water bridges: B:G.194 Salt bridges: B:R.189 pi-Stacking: B:Y.195

1 x CA: CALCIUM ION(Non-covalent)

CA.2: 4 residues within 4Å: Chain B: C.233, L.235, V.238 Ligands: DC-DA-DG-DG-DT-DC-DT-DA-DC.1 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.233, B:L.235, B:V.238

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 11 residues within 4Å: Chain B: L.31, P.32, S.33, G.34, S.36, F.37, R.38, W.39, R.40, I.144, T.148 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:P.32, B:G.34, B:S.36, B:W.39, B:T.148 Water bridges: B:S.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, A. et al., Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA. Nature (2005)

Release Date

2005-04-05

Peptides

N-glycosylase/DNA lyase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

N-glycosylase/DNA lyase