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Figure 4.
Figure 4. Position of Key Protein Residues in Closed
Polymerase Complexes with Correct or Incorrect Incoming
Nucleotides
(A) Two views (major groove view, top;
−90° rotation of the top view, bottom) of the nascent base
pair of the mismatch structure (dG-dAMPCPP; green carbons)
superimposed (see Figure 1) with that for a correctly matched
base pair (gray carbons). The templating base is omitted from
the correctly matched overlay for clarity. The structure
illustrates the position of key protein side chains that can
influence catalytic behavior. For catalytic activation with the
correct incoming nucleotide, N subdomain closing is associated
with the loss of a salt bridge between Arg258 (R258) and Asp192
(D192), which coordinate both active-site metals (M^2+), and the
formation of hydrogen bonds (black dashed lines) with Glu295
(E295) and Tyr296 (Y296). Phe272 (F272) is repositioned in the
closed complex to insulate Asp192 from Arg258. Arg283 (R283)
that is situated in the N subdomain interacts with the minor
groove edge of the templating strand (not shown). With an
incorrect incoming nucleotide, R258 and R283 are in
conformations that preclude catalytic activation. Arg283 is
observed to hydrogen bond with the minor groove edge and
phosphate backbone of the templating base. Other key residues
(Asp192, Asn279, and Phe272) are observed in similar positions
as that found with a correct incoming nucleotide.
(B) Major
groove view of the nascent base pair of the dG/dC-dAMPCPP
superimposed mismatch structures (dC template, light blue
carbons; dG template, green carbons).
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