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Figure 2.
Figure 2. The Polymerase Active Site(A) The backbones of
the polymerase palm and fingers domains are shown as magenta and
blue ribbons. The carbon atoms of the polymerase side chains
shown in stick form are white, while those of the DNA template
are dark gray, and those of the primer DNA and dTTP are gold.
The bound calcium atoms are shown as light blue mesh spheres,
labeled A and B according to their catalytic function. Hydrogen
bonds are shown as green lines, while interactions with the
metal ions are blue lines. This view looks down the length of
the fingers, roughly 180° away from the orientation of
Figure 1A.(B) The KKRY motif (residues 705–708) interacts with
the primer-template duplex next to the polymerase active site.
Residues 703–708 are shown; Thr 703 and Gly 704 are not
conserved in the pol α family. Asp 621 from Figure 2A is shown
as an isolated side chain. Only the last two bases of the primer
strand are shown for clarity. The orientation of this figure can
be related to that of Figure 2A by comparing the primer-template
DNA
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