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. Author manuscript; available in PMC: 2015 Mar 1.
Published in final edited form as: Nat Chem Biol. 2014 Aug 3;10(9):780–786. doi: 10.1038/nchembio.1606

Figure 2. Folding topologies adopted by the bubble and pseudoknot segments and their flanking stem segments in the structure of T. tengcongensis ydaO riboswitch bound to c-di-AMP.

Figure 2

a, b, Schematic (panel a) and folding topology (panel b) of the bubble segment (in grey) relative to flanking stems P2 (in purple) and P3 (in cyan) in the ydaO riboswitch complex. Key Watson-Crick pairs C32-G96 and G39-C94 are shown in red. The bound Mg2+ cation is shown as a green-colored ball. c, Octahedral coordination geometry of the Mg2+ cation (in green), with bound water molecules represented by red-colored balls. d, Pairing alignments of major groove-aligned G92•(G39-C94) base triple. Note that C94 adopts a syn alignment. e, f, Schematic (panel e) and folding topology (panel f) of the pseudoknot duplex segment (in blue) relative to flanking stems P1 (in green) and P5 (in orange) in the ydaO riboswitch complex. g, Pairing alignment within a tetrad formed by the long range Hoogsteen A73•U112 pair aligning with the minor groove edge of the Watson-Crick C5-G111 pair.