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Figure 4.
Figure 4. Modeling Deminated Bases into the Protein(A)
Uridine5'monophosphate (dUMP). It is possible to see the binding
between the R142 and the sulfate ion that mimics the phosphate
in the 5' position, the hydrogen bonds that fix the position of
R464 and N161 and would be expected to discriminate between
oxygen or amino group, i.e., uracil or cytosine base, and the
position of Y158, which could contribute to steric
discrimination against the thymine methyl group.(B)
Hypoxanthine. The oxygen in position 6 on hypoxanthine could be
recognized in same way as the oxygen in position 4 of uracil.
Only the hypoxanthine nucleoside is shown to highlight the
position of the sulfate ion. The dUMP and the hypoxanthine were
positioned manually to maximize hydrogen bonding and minimize
steric clashes.
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