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Figure 2.
Figure 2. Overall Architecture of the Complex(a) The
overall architecture of the complex. The green polypeptide and
the red polypeptides are the upstream and downstream subunits,
respectively. Zincs are shown as gray spheres. The conserved
AGGTCA half-sites are shown in purple, and the 5′ flanking
base pairs and spacer are shown in yellow.(b) Surface
representation of the protein–DNA complex. The view is nearly
identical to that shown in (a). The location of the Grip box in
the minor groove is indicated.(c) Stereo diagram of the overall
complex, showing the side chains (in yellow) mediating direct
protein–DNA contacts and those coordinating the zinc ions (in
pink). The green polypeptide is the upstream subunit. The yellow
spheres are zincs, and their coordinating cysteines are in pink.
The numbers along the DNA indicate the sequence as shown in
Figure 1c.Half-Site Contacts(d and e) Schematic summary of
upstream (d) and downstream (e) contacts between the core DBD
and the half-sites. Red arrows indicate hydrogen bonding to the
DNA phosphates; black arrows indicate other hydrogen bonds. The
arrowhead indicates the probable hydrogen-bond acceptor. The
contacts involve the side chains, unless otherwise stated. Amino
acids in black make at least one direct hydrogen bond to the DNA
bases. Residues circled in green make different DNA interactions
in the two subunits. The blue circles are water molecules that
mediate protein–DNA contacts. The yellow base pairs are
different in steroid-receptor response elements. The DNA shown
is underwound for clarity.
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