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. Author manuscript; available in PMC: 2011 Dec 27.
Published in final edited form as: J Phys Chem B. 2010 Nov 10;114(48):15991–16002. doi: 10.1021/jp107193z

Figure 2.

Figure 2

A) Base-libration of U38 (light blue) relative to its pair-based nucleotide A27; the C5 (red) and C6 (dark blue) atoms are shown. The total amplitude of the best-fit base-libration model was found to be ±4o, corresponding to an 8° total angular excursion. B) Conformational exchange carries U38 (blue) within the entire upper helix between two distinct conformational states. Shown here is the transformation from the C frame to the M frame. The z axis of the C frame is indicated by the dotted line, and it is approximately perpendicular to the plane of the U38 base in 1ANR. The localized libration of the U38 base shown in Figure 2A is generated by a ±4o rotation about the zC axis. A bend of the entire upper helix is rendered by a rotation about yM and a twist and is affected by a rotation about zM. Both rotations are indicated in this figure.