NMR structure of a 4 × 4 nucleotide RNA internal loop from an R2 retrotransposon: Identification of a three purine–purine sheared pair motif and comparison to MC-SYM predictions

Potential hydrogen bonds or electrostatic interactions in the B. mori R2 internal loop, 5′AAG/3′AGG, and in 5′GAA/3′AGG. (A) G17 amino proton and G16 imino proton share negative charge of a nonbridging phosphate oxygen on A5. The same interaction is observed in 5′CGAAG/3′GAGGU (Chen et al. 2005), but the distances are ∼1 Å farther in 5′CGAAG/3′GAGGC (Kazantsev et al. 2005). (B) Comparison of electrostatic interactions in the G6G16 pair of the R2 loop with the equivalent AG pair in 5′CGAAG/3′GAGGU (Chen et al. 2005). Interaction of G6 carbonyl oxygen with cross-strand 2′-OH proton (left) is replaced by interaction of A amino proton with cross-strand 2′-OH oxygen.