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Figure 5.
Figure 5. Stereo diagrams of the average structure of AD3
RNA. (a) The average structure of AD3 with regions of
noncanonical structure elements shaded according to the
color-coding in Figure 1c: helices IV and V are colored gray,
the palindromic ends of loop E are yellow, the central base
pairs of loop E are dark blue, the tandem GU wobbles purple, and
loop D is colored green. (b) A heavy-atom only, CPK,
space-filling representation of the average structure of AD3.
Atoms are colored by type (nitrogen in blue, oxygen in red,
phosphorus in magenta and carbon in gray). Superposition of (c)
the loop E residues (72-78, 98-104) and (d) loop D-helix IV
residues (79-97) from the nine structures generated by TAMD on
the average structure. The average pairwise root mean square
deviation between each structure and the average for loop E
residues and loop D-helix IV residues is 0.90 Å and 0.55 Å,
respectively.
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