Fig. 2: Analysis of preQ1-I riboswitch structures in the light of reactivity prediction.
From: A natural riboswitch scaffold with self-methylation activity
a Sequence and secondary structure of the Tt preQ1-I riboswitch (minimal aptamer motif in black). b Cartoon representation of the three-dimensional fold of the preQ1-bound aptamer (pdb code 3Q50; DOI: 10.2210/pdb3q50/pdb). c Stick representation of the ligand-free pocket revealing that A14 slides into the pocket and fills the space of preQ1 while C15 flips out and becomes exposed (pdb code 3Q51; DOI: 10.2210/pdb3q51/pdb). d Stick representation of the preQ1-bound riboswitch pocket with crucial atom numbers annotated in black. e Chemical structures illustrating the hydrogen bond network of preQ1 in the riboswitch pocket and the 2’-OH group of G11 that comes close the Hoogsteen face of preQ1. f Structure of a putative base pair between C15 (imino tautomer) and m6preQ1 in the preQ1-I riboswitch pocket.
