Structure and thermodynamics of a UGG motif interacting with Ba²⁺ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)–G(syn) pair

Noncanonical base pairs observed in crystallographic models of the AUGUGGCAU duplex. (A,C) The U·G wobble interacting with solvent molecules. (B) Stick representation of the G(anti)–G(syn) pair and (D) G(syn)–G(syn) base pairs. The stacking interactions observed for G–G (E) and U·G pairs (F). Panels A and B are based on the unliganded structure; C–F are based on the Ba(2) model. Water molecules are red spheres, Ba²⁺ ions are green, and Na⁺ is blue. The 2F_o–F_c electron density map (gray) is contoured at the 1σ level. The H-bonds are black dashed lines.