SMTL ID : 2hhx.1

O6-methyl-guanine in the polymerase template preinsertion site

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.26 Å

Oligo State

monomer

Ligands

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

DC-DC-DT-DG-DA-DC-DT-DC-DG.1: 29 residues within 4Å: Chain A: C.5, G.6, A.7, G.8, T.9, C.10, A.11, G.12, G.13 Chain B: P.235, T.260, S.261, A.262, L.279, R.282, K.286, Y.291, R.319, Q.328, N.329, I.330, P.331, I.332, R.333, Y.418, Q.501, V.532, H.533, D.534 Protein-ligand interaction information (PLIP) not available

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

GLC-FRU.2: 10 residues within 4Å: Chain A: A.11, G.12 Chain B: E.219, Y.223, E.229, F.230, N.231, I.232, N.233, Y.281 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.229, B:N.231, B:E.219, B:Y.223, B:N.231, B:I.232, B:N.233, B:N.233 Water bridges: B:Q.237 GLC-FRU.3: 8 residues within 4Å: Chain B: E.29, Y.31, D.76, R.79, L.99, D.112, I.309, N.311 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.79, B:D.112, B:N.311, B:N.311, B:A.313, B:R.79 Water bridges: B:Q.312

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

SO4.4: 3 residues within 4Å: Chain B: H.386, R.406, K.410 3 PLIP interactions: 3 interactions with chain B Water bridges: B:Q.360 Salt bridges: B:R.406, B:K.410 SO4.5: 1 residues within 4Å: Chain B: R.523 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.523 Salt bridges: B:R.523 SO4.6: 3 residues within 4Å: Chain B: M.3, A.4, R.47 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:A.4 Water bridges: B:R.47 Salt bridges: B:R.47 SO4.7: 6 residues within 4Å: Chain B: I.332, A.355, D.357, E.535, H.571, A.579 1 PLIP interactions: 1 interactions with chain B Water bridges: B:R.341

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: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

DNA Polymerase I

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