SMTL ID : 1q3f.1

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

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

DT-DG-DT-NRI-DA-DT-DC-DT-DT.1: 29 residues within 4Å: Chain A: A.1, A.2, A.3, G.4, A.5, T.6, A.7, A.8, C.9, A.10 Chain B: Q.63, D.64, P.65, Y.66, H.67, P.86, P.87, S.88, A.133, G.165, S.166, A.186, H.187, S.189, P.190, L.191, S.192, R.195 Ligands: URA.2 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.194, B:Q.63, B:S.88, B:S.88 Water bridges: B:R.195, B:D.64, B:H.67, B:Q.71, B:Q.71, B:N.134

1 x URA: URACIL(Non-covalent)

URA.2: 10 residues within 4Å: Chain B: G.62, Q.63, D.64, P.65, Y.66, C.76, F.77, N.123, H.187 Ligands: DT-DG-DT-NRI-DA-DT-DC-DT-DT.1 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.77 Hydrogen bonds: B:Q.63, B:D.64, B:F.77, B:N.123, B:N.123, B:H.187 pi-Stacking: B:Y.66

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain B: R.32, Y.35, T.36, V.37 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:V.37, B:V.37 Water bridges: B:R.32, B:R.32, B:R.32 Salt bridges: B:R.32

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bianchet, M.A. et al., Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase. Biochemistry (2003)

Release Date

2004-03-23

Peptides

Uracil-DNA glycosylase: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Uracil-DNA glycosylase

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