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Figure 2.
Fig. 2. Pyr bound in the PvDHFR active site. The Pyr and
NADPH cofactor are shown as balls and sticks with carbon,
nitrogen, and chlorine colored yellow, blue, and magenta,
respectively. (A) Pyr binding with the WT PvDHFR. Interactions
between the enzyme and the pyrimidine ring of the inhibitor
include electrostatic interactions and H-bonds indicated by
dotted lines. Numbers next to the lines indicate distances in
Å. (B) Pyr binding with the SP21 double-mutant PvDHFR.
Interactions around the pyrimidine ring are similar to the WT
enzyme. The mutation at codon 117 from Ser to Asn increases a
steric factor in the active site, and, as a result, the
positions of both NADPH and Pyr are perturbed from their optimum
binding, reducing the efficiency of Pyr by as much as 300-fold.
(C) Superposition of Pyr-binding sites in the WT PvDHFR (green)
and the SP21 double-mutant enzyme (orange) with a rmsd of 0.53
Å. While the position of pyrimidine is held in the same
place, the mutation at S117N causes the displacement of
p-chlorophenyl moiety of Pyr from its optimal binding with the
p-Cl atom shifted by 1.1 Å and the torsion plane between
the two rings twisted by -32°. The mutation also caused a
local main-chain movement of residues 118 -125 (0.60 -1.88
Å), with respect to the WT enzyme. The mutation at codon
58 from Ser to Arg is not in proximity with the Pyr-binding site.
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