Figure 2.
FIGURE 2. Drug binding to BmrR. Key residues are labeled
and shown as pale blue sticks with the oxygen atoms colored red
and nitrogen atoms colored blue. Secondary structural elements
are depicted as pale blue ribbons (coils, helices; arrows, β
strands). A, wtBmrR-imidazole-DNA complex (21). Imidazole
molecules are shown as green sticks, and dashed lines denote
hydrogens bonds. B, wtBmrR-R6G-DNA complex. R6G is shown as red
sticks with its positive charge depicted by a red +.
Electrostatic interactions are shown as dashed lines. C,
wtBmrR-Ber-DNA complex. Ber is shown as yellow sticks, and its
positive charge depicted by a blue +. Electrostatic interactions
are shown as dashed lines. D, superposition of the
BmrR-imidazole-DNA and BmrR-R6G-DNA complexes. E, superposition
of all BmrR-drug-DNA complexes. TPP^+ is shown as green sticks
with its positively charged phosphorus atom colored purple. F,
superposition of E253Q-DNA and BmrR-R6G-DNA structures.
E253Q-DNA is shown as green ribbons and sticks. Dashed lines
indicate potential clashes between R6G and residues in the E253Q
structure. Figs. 2, 3, 4, 5 and 6 were made with PyMol (Delano,
W. L. (2002)).
helices; arrows, β
strands). A, wtBmrR-imidazole-DNA complex (21). Imidazole
molecules are shown as green sticks, and dashed lines denote
hydrogens bonds. B, wtBmrR-R6G-DNA complex. R6G is shown as red
sticks with its positive charge depicted by a red +.
Electrostatic interactions are shown as dashed lines. C,
wtBmrR-Ber-DNA complex. Ber is shown as yellow sticks, and its
positive charge depicted by a blue +. Electrostatic interactions
are shown as dashed lines. D, superposition of the
BmrR-imidazole-DNA and BmrR-R6G-DNA complexes. E, superposition
of all BmrR-drug-DNA complexes. TPP^+ is shown as green sticks
with its positively charged phosphorus atom colored purple. F,
superposition of E253Q-DNA and BmrR-R6G-DNA structures.
E253Q-DNA is shown as green ribbons and sticks. Dashed lines
indicate potential clashes between R6G and residues in the E253Q
structure. Figs. 2, 3, 4, 5 and 6 were made with PyMol (Delano,
W. L. (2002)).