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Figure 7.
Figure 7 Influence of Gly 568 on DNA binding to the polymerase
active site. Column (I) shows the event of nucleotide insertion
opposite an unmodified template strand with adenine in the
active site, while column (II) depicts the case of a template
containing an abasic site as in the AP:dG complex. Vertical
arrows specify the strained (red) or the relaxed state (green),
respectively. Diagonal arrows indicate whether the polymerase is
in the closed (red) or open conformation (green). The template
strand is depicted in magenta and the incoming nucleotide in
green. The yellow box indicates the position of Gly 568. (IA)
and (IIA) show the polymerase in the strained state and the open
conformation. Transition into the relaxed state presumably
causes the adenine base of the unmodified template to be pushed
back (IB), while the AP-containing template is unaffected (IIB).
(IC) and (IIC) depict an incoming dNTP bound to the base of the
fingers domains. Transition to the closed and strained
conformation ensures the correct positioning of all residues to
enable the catalytic phosphodiester bond formation (ID). In the
case of AP, a closed and relaxed conformation is feasible (IID).
The missing complementary base causes the dNTP to be held in
place less tightly and phosphodiester bond formation is less
efficient (IIE).
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