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Figure 3.
Figure 3. Structures of UP1-oligonucleotide complexes for
substitution of adenine 9. 2F[o] -F[c] composite omit electron
density maps contoured at 1.25 s. Chevrons indicate the hydrogen
bonding network. (a) Wild-type structure with Ade9 shown making
hydrogen bonding contacts to the Arg178 guanidinium group
through its N7 (2.7 Å) and from the main-chain carbonyl of
Lys179 (3.0 Å). Ade9 is stacked directly over the
conserved Phe108 of the RNP2 consensus sequence. (b) The
UP1-A(9)Neb structure showed no substantive changes in either
protein or DNA structures. The absence of the N6 amino group
allowed the base to move slightly closer to Arg178 (2.5
Å). (c) UP1-A(9)7deazaA structure shows a large
conformational rearrangement of the Arg178 side-chain. The
Arg178 guanidinium group shifted 9.1 Å away from its
position in the wild-type structure where it makes contacts to
the O2 of Thy8 and N7 of Ade9 to make a new set of contacts to
Glu93. All electron density Figures were made using PYMOL
(DeLano Scientific, CA).
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