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Figure 4.
Fig. 4. Polymerase active site. (A) Stereoribbon
representation (using color code as in Fig. 2) with modeled DNA.
Active-site residues are shown as ball-and-stick representations
with carbon (green), nitrogen (blue), and oxygen (red) atoms.
The DNA template (light brown), primer (light brown), and dNTP
(orange) complex has been taken from the coordinates of T7
replication complex (15) by superimposing D404, D542, and
adjacent residues with corresponding residues in T7 pol (D475
and D654). Phosphorus atoms are yellow. The two metals of the T7
replication complex are shown as magenta spheres. (B)
Experimentally observed metal-binding site for Mn^2+ (F[o]  F[c]
density contoured at 5  ) and Zn^2+
in the "low salt" crystal form. The carboxylates E578 and E580
are conserved in type B polymerases (Fig. 3).
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