FIGURE 3.

Ribose and ion interactions stabilize pseudoknot. (A) Interactions between the 2′-OH groups of G13493 and U13494 with the A13537 nucleobase are shown, along with the ribose zipper hydrogen bonding between 2′-OH groups of C13495 and C13536. (B) Interactions between a cobalt(III) hexammine with the O6 and N7 of G13493 and G13484. (C) Interactions among a hydrated Mg²⁺, K⁺, and four tiers of base pairs within the major groove. Distances (Å) are shown for the oxygen ligand shared between the Mg²⁺ and K⁺ in a µ-oxo arrangement. Hydrogen bonds between the hydrated Mg²⁺ and base pairs are colored black, K⁺-ligand bonds are represented by dotted red lines, and the µ-oxo bond involving K⁺ is represented by a thick dotted line. Yellow mesh shows a portion of the anomalous difference Fourier synthesis calculated with 1.771 Å X-ray data (Table 1), contoured at 3 σ.