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Figure 6.
Figure 6. (a) Stereo view of the A[(n
-1)]·C^+·G-C[n] base quadruple in the average
structure of the PEMV-1 pseudoknot formed by loop 1 and stem 2
(A[12]·C[10]^+·G[28]-C[13]). C[10] is shown in
red, the accepting Watson-Crick pair in blue, and A[12] of stem
2 which forms the third hydrogen bond to C[10]^+. (b) The
three-base reverse turn places C[10] in the proper orientation
to form the A[(n -1)]·C^+·G-C[n] base quadruple.
C[10] is shown in red, U[9] from the Hoogsteen wedge pair in
yellow and G[11], which forms the closing base-pair of stem 2,
in blue. (c) Superposition of the bases from the A[(n
-1)]·C^+·G-C[n] quadruples from the BWYV
pseudoknot (white, 437D),[9.] the HDV ribozyme (red, 1CX0) [22.]
and the average structure of the PEMV-1 pseudoknot (blue). (d)
Overlay of the heavy atoms of the base quadruples and
intervening nucleotide from the HDV ribozyme (red, residues
141-144, 161 of 1CX0) [22.] and the PEMV-1 pseudoknot (blue,
residues 10-13, 28).
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