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Figure 4.
Figure 4. Details of PAP1−DNA interactions. a, Close up
view of the hydrophobic interactions (dotted lines) between Phe
93 and the two thymine methyl groups of the TT base pair step.
b, Comparison of the side chain conformational changes in the
Pap1 and GCN4 bZIP basic regions. The Pap1 side chains (yellow)
are superimposed on the GCN4 side chains (green). Hydrogen bonds
are indicated by solid lines, with the buried water molecule
bridging Gln 90 and the main chain of Asn 86. c, Close up view
of the Pap1 bZIP basic region, with the buried water molecule
bridging Gln 90 and the main chain of Asn 86. The water molecule
also forms hydrogen bonds with the DNA bases. d, Comparison of
the side chains of conserved residues of Pap1 (yellow) with the
corresponding residues of GCN4 (green).
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