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Figure 3.
Figure 3. DNA recognition of the Pap1 bZIP motif. a, Stereo
view of the basic region of the Pap1 bZIP bound to the major
groove of its DNA half site. Hydrogen bonds and van der Waals
contacts between protein and DNA are indicated by solid and
dotted lines, respectively. b, Diagrams showing protein−DNA
interactions in the Pap1−DNA (left) and the GCN4−DNA (right)
complexes. Each half site of the DNA is shown. Hydrogen bonds
and van der Waals contacts between protein and DNA bases are
indicated by solid and dotted black lines, respectively.
Interactions with the DNA phosphate backbones are indicated with
green lines. c, Schematic representations of DNA recognition by
the GCN4 bZIP (left), Pap1 bZIP (middle), and PHO4 bHLH (right)
motifs. The conserved amino acid side chains of the motifs that
make direct contacts with the DNA bases of the core sequences
are shown. Hydrogen bonds are indicated with broken lines and
van der Waals contacts with dotted lines. For clarity, water
mediated hydrogen bonds are omitted.
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