SMTL ID : 1emj.1

URACIL-DNA GLYCOSYLASE BOUND TO DNA CONTAINING A 4'-THIO-2'DEOXYURIDINE ANALOG PRODUCT

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

DT-DG-DT-ASU-DA-DT-DC-DT-DT.1: 28 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, 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 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.63, B:D.64, B:S.88, B:Y.194 Water bridges: B:Q.71, B:Q.71, B:E.138

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-ASU-DA-DT-DC-DT-DT.1 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Q.63, B:D.64, B:F.77, B:N.123, B:N.123, B:H.187 Water bridges: B:Y.66 pi-Stacking: B:Y.66, B:F.77

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parikh, S.S. et al., Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-05-16

Peptides

URACIL-DNA GLYCOSYLASE: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

URACIL-DNA GLYCOSYLASE

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