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Figure 3.
Fig. 3. Conformational interlocks during DNA synthesis. A
schematic overview of the polymerase active site (A) and atomic
coordinates (B) derived from the open and closed BF structures
represent a complete round of DNA synthesis. The conformational
changes described here are presented in animated form in Movie
1, which is published as supporting information on the PNAS web
site. The reaction cycle starts with the acceptor template base
(n, red) bound at the template preinsertion site (between the O
and O1 helices; green shading); Tyr-714 blocks access to the
insertion site (blue shading) and stacks with the n-1 base pair
at the postinsertion site (gray shading). Formation of the
closed conformation involves rearrangement of the O and O1
helices, which simultaneously blocks the template preinsertion
site and unblocks the insertion site. These rearrangements move
the acceptor template base (n) to the insertion site, where it
pairs with an incoming dNTP (green). Nucleotide incorporation
occurs on formation of a cognate base pair and proper assembly
of the catalytic site (orange shading). The cycle is completed
with translocation of the DNA by one base pair position. The
polymerase resets to the open conformation in preparation for
the next round of DNA synthesis.
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