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Figure 3.
Figure 3. (a) Structure of the polymerase active site region
of HIV-1 RT including the primer grip. Secondary structural
elements of the p66 palm subdomain are shown as red ribbons. The
three catalytically essential aspartic acid residues (Asp110,
Asp185, and Asp186) are shown with cyan side-chains. Tyr183 and
Met184, which form part of the conserved YMDD motif, are shown
with gold side-chains. Amino acid residues at the primer grip
are shown in green. The dsDNA is shown with the template strand
in dark gray and the primer strand in light gray. (b) A
schematic diagram showing interactions between the 3′-terminal
nucleotide of the primer strand (Pri1) and amino acid residues
at the polymerase active site, with selected distances given in
Å. Hydrogen-bonding interactions between the side-chain
O^δ1 atom of Asp185 and the 3′-OH of Pri1, and between the
amide nitrogen atom of Met230 of the primer grip and the
phosphate oxygen atom of Pri1 are indicated by heavy lines.
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