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Figure 1.
FIG. 1. A, ribbons diagram (50) of UP1 bound to the
sequence d(TTAGGGTTAGGG). Two copies of UP1 form a
crystallographic dimer in which the DNA is bound in an
anti-parallel arrangement across RRM1 (residues 1-92) and RRM2
(residues 93-195) from the two UP1 molecules. The 2-fold
rotation of the UP1 molecules into the crystallographic dimer
permits the formation of a contiguous single-stranded nucleic
acid binding cleft. Previous studies have shown that UP1 has an
RNA binding site size of 15 nucleotides, which is in good
agreement with the structure. The positions of the 6-MI
substitutions in oligonucleotides TR2-6F and TR2-11F are
indicated (circles). B, 2F[o] - F[c] electron density from a
composite omit map of 6-MI substituted for Gua-11 (TR2-11F)
contoured at 1.2  . C, electron density
of 6-MI from a 2F[o] - F[c] composite omit map generated using
phases obtained from molecular replacement of UP1 bound to
d(TTAGGGTTAGGG) contoured at 1.2 . The model shows the
position of 6-MI in TR2-6F (blue). The electron density
corresponding to the phosphodiester and deoxyribose atoms at
position six are of good quality, whereas the highly mobile base
appears only weakly. This finding is consistent with electron
density maps derived from the wild-type structure that was
resolved in our laboratory for comparison. In both the original
and substituted DNA, the base at position 11 stacks with Gua-10
and makes interactions through the base O6 (O4 in 6-MI) to the
main chain of UP1. In contrast to TR2-6F, the electron density
of 6-MI in TR2-11F is moderately well ordered.
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