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Figure 3.
Fig. 3. Electrostatic charge distribution and binding pockets.
Delphi electrostatic potential calculated and mapped onto the
Connelly solvent accessible surface using InsightII calculated
with coordinates corresponding to the core domain (residues 1379
to 1625). Simulated ionic strength was set to 0.145 M with a
bulk solvent dielectric constant of 80. The first seven
NH[2]-terminal residues from a symmetry-equivalent molecule are
shown as a green stick model. The first three residues (1359 to
1361) are visible binding into the putative acetyllysine
recognition pocket of the first domain. (A) Orientation of the
hTAF[II]250-DBD is the same as that of Fig. 2. Numerous
clustered lysine and arginine residues result in an extended
basic surface. (B) Reverse side of the double bromodomain
relative to (A) displaying the acidic stripe present running
across the top of the molecule. (C) Putative binding surface of
the double bromodomain viewed from the bottom surface of (A).
Two deep pits (labeled) at the center of each four-helix bundle
are readily apparent and are separated by about 25 Å.
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