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Figure 8.
Figure 8. (a) Overlay of the 15 lowest energy structures of
the PEMV-1 pseudoknot with loop 2 (green) and U[14] (purple)
highlighted. (b) Details of the A[25], A[26], and A[27]
non-canonical base-pairings between loop 2 (green) and stem 1
(blue) nucleotides. A[25] forms an N1-2' OH hydrogen bond with
the sugar of C[16], A[27] forms the analogous interaction with
the sugar of C[15], and A[26] forms a pair of reciprocal
hydrogen bonds with G[8] from stem 1 (A[26] amino to G[8] N3,
G[8] amino to A[26] N1, shown with donors in red, acceptors in
blue).
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