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. 2005 Dec 23;33(22):6992–6999. doi: 10.1093/nar/gki992

Figure 4.

Figure 4

Comparison of predicted 12 and 14mer RNA complex structures. Structures are averages obtained from MD simulations. The top panels show the RNAs without FMN; the bottom panels show the RNAs as surface representations with the ligand as a tube structure. (A) The 14mer forms a binding pocket that encapsulates FMN tightly and shields its flavin ring from contact with solvent water molecules. (B) The 12mer loses stability that had been conferred by the three hydrogen bonds formed by the sheared A4·G11 N7-amino, amino-N3 non-Watson–Crick base pair of the 14mer. The 5′ and 3′ ends of the RNA become separated, leaving FMN with no hydrogen bonds to the adenine residue A11 (corresponding to A13 of 14mer) and exposed to solvent water molecules.