Fig. 2
From: Structure-based insights into self-cleavage by a four-way junctional twister-sister ribozyme
Tertiary interactions in the structure of the twister-sister ribozyme. a, b Tertiary interactions formed at the four-way junction. One hydrated Mg2+ (labeled M5) is coordinated directly to the pro-S P non-bridging phosphate oxygens of G55–G56 and C24–G25 steps, whereas the pro-R P non-bridging phosphate oxygens form hydrogen bonds with the 2′-OH groups of G55 and C24. One inner-sphere hydration water of M5 forms a hydrogen bond with N7 of G25, whereas another inner-sphere hydration water of M5 forms two hydrogen bonds with G35. c, d Continuous stacking interactions within the four-way junctional region. A7, which is extruded from L1, forms stacking (c) and hydrogen bond (d) interactions with the zipped-up SL4 loop segment. e–g Stacked bases G35 and U36, which are extruded from SL4, interact with stem P2 and L1 (e). Extruded G35 forms one hydrogen bond with the major groove edge of the Watson–Crick G56–C12 pair (f). Extruded U36 forms two hydrogen bonds with the inner-sphere waters of two hydrated Mg2+ ions, in which one is coordinated with O6 of G59 and the other is coordinated with the non-bridging phosphate oxygens of residues A8 and A9 (g)
