Fig. 2: Structural details of the SAM-VI riboswitch pocket bound to SAM.
From: SAM-VI riboswitch structure and signature for ligand discrimination
a RNA surface representation shows the cavity for the adenine base of the SAM ligand buried into the RNA and the methionine moiety directed outwards. b–e Different views on the binding pocket interactions with ligand SAM (for discussion see main text). f Detailed view of the SAM-adenine U8 base pair. The composite omit electron-density map of SAM contoured at the 1.0 σ level is shown in light gray. g Detailed view on the sulfonium moiety and the nearest neighbors (O4 U6 and O4 U8) with selected distances indicated by dotted lines and corresponding values in Å. The composite omit electron-density map of SAM contoured at the 1.0 σ level is shown in light grey. h Binding pocket of the U6C-mutant SAM-VI riboswitch: U6C moves away from the sulfonium moiety; note that a water molecule appears and takes over the role of the mutated U6; distance values are in Å. The composite omit electron-density map of SAM contoured at the 1.0 σ level is shown in light gray.
