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Figure 3.
Figure 3. DNA Polymerase b Ternary Complex with
8-OxodG-dCTP(A) 2F[o] - F[c] electron density map contoured at 1
s (black), superimposed on the refined model. Additionally, a
difference map was calculated, omitting O8 and contoured at 3.3
s. Negative density (red) is visible at the 8-oxy position of
the template base, demonstrating unbiased evidence of the
presence of the additional oxygen. The ternary complex with an
8-oxodG template base is very similar to the previously
determined ternary complex containing undamaged deoxyguanine
paired with ddCTP [12]. The modified guanine is in the standard
anti conformation, and dCTP is bound with a coordinating Mg2+
atom (data not shown).(B) Comparison of the 5'-phosphate
backbone conformation of 8-oxodG relative to that observed in
the structure of pol b with an unmodified deoxyguanine in the
polymerase active site (orange) [12]. The presence of the sharp
bend along with limited enzyme contacts with this phosphate
enables flipping of the phosphate away from the carbonyl oxygen
at C8 of 8-oxodG. The backbone a torsion angle (O3'-P-O5'-C5')
of the templating guanine is altered 184° when a carbonyl group
is introduced at C8. In addition, the Lys280 side chain
position, but not that of Asp276, is altered in the presence of
8-oxodG.
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