SMTL ID : 2hhv.1

T:O6-methyl-guanine in the polymerase-2 basepair position

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

2 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 10 residues within 4Å: Chain C: E.29, N.30, Y.31, D.76, R.79, L.99, D.112, I.309, N.311, T.323 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.79, C:D.112, C:N.311, C:N.311, C:A.313, C:R.79 Water bridges: C:D.76, C:R.79, C:Q.312 GLC-FRU.2: 5 residues within 4Å: Chain C: E.455, V.458, K.462, R.488, E.492 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:E.455, C:K.462, C:K.462, C:E.492 Water bridges: C:E.455, C:E.492, C:E.492, C:R.488, C:R.488, C:E.492, C:E.492

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain C: H.386, R.406, K.410 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Q.360 Salt bridges: C:R.406, C:K.410 SO4.4: 1 residues within 4Å: Chain C: R.523 2 PLIP interactions: 2 interactions with chain C Water bridges: C:R.523 Salt bridges: C:R.523 SO4.5: 4 residues within 4Å: Chain C: K.2, M.3, A.4, R.47 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.4 Salt bridges: C:R.47 SO4.6: 2 residues within 4Å: Chain C: S.432, R.433 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.433 Water bridges: C:S.432, C:K.434 Salt bridges: C:R.433 SO4.7: 4 residues within 4Å: Chain C: I.420, S.421, D.422, I.440 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.420, C:D.422, C:D.422

1 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 3 residues within 4Å: Chain C: D.357, Y.358, D.534 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.357, C:Y.358, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Warren, J.J. et al., The structural basis for the mutagenicity of O6-methyl-guanine lesions. Proc.Natl.Acad.Sci.Usa (2006)

Release Date

2006-12-12

Peptides

DNA Polymerase I: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

C
A

DNA Polymerase I

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