Chemical shift perturbations from MgCl2 titration mapped onto the D5-PL solution NMR structure. Changes in chemical shift between free D5-PL and 10 mM bound D5-PL as a function of nucleotide sequence in the (A) ribose C1′, (B) aromatic carbon, and (C) aromatic nitrogen regions of D5-PL. Shown to the right of each panel are the configurations of the standard Watson-Crick base pairs for G–C and A–U as well as the wobble GU pair. The base and the ribose atoms probed in this study are highlighted as spheres, and the edges facing the deep major grooves and shallow minor grooves of RNA helices are indicated. Projection of the Mg2+ ion binding onto the D5 solution NMR structure indicates that metal ion binding occurs in both the major and minor grooves of the tetraloop and bulge regions (E,G), but only in the major groove of the triad (E,G). Shown also for comparison are the electrostatic calculations (D,F) taken from Figure5, A and D.
