FIGURE 8.

Structural interactions suggested by the crystal structure (Shechner et al. 2009) and confirmed as functionally significant by NAIM and DMS interference experiments. (A) Contacts with structural metals near (left) A31–A32, (middle) G45–C47, and (right) G75–G77. Pro-R_p phosphate oxygens for which phosphorothioate NAIM interference was significant are shown as larger gray spheres; pro-S_p oxygens are not accessible to NAIM (Verma and Eckstein 1998). Meshes represent simulated-annealing |F_obs|-|F_calc| OMIT maps in which the hydrated metal clusters were excluded from map calculations, contoured at (left) 4σ, and (middle, right) 2.5σ. Black dashed lines indicate hydrogen bonds. Solid lines bound to Mg²⁺ ions indicate proposed inner-sphere contacts. (B) Wall-eyed stereograph highlighting interactions between J1/3 and the P3–P6–P7 domain. Functional groups showing significant interference in biochemical experiments are shown as larger spheres, colored white for 2′-deoxy interference, gray for phosphorothioate interference, and black for DMS interference. (C) Individual base triples or quadruples involved in this interaction, rendered as in B.