Figure 2: Identification of driver and anchor atoms with apo and bound riboswitches.

(A) Global view. (B) Zoomed-in at the preQ1-binding region. The driver atom is labeled as a cyan sphere and the anchor atom is labeled as a magenta sphere. The base that interacts with the driver atoms is A50. Bases that interact with anchor atoms are G7 and U19. Riboswitch is represented as ribbon, with the backbone phosphate atom embedded as spheres. The ligand is depicted as stick. The dark color of the ribbons indicates regions with large conformational changes, where the global backbone displacement (GBD) of corresponding pairs is greater than a preset distance (3.5 Å). Side chains depicted as lines are shown only for residues in contact with the riboswitch’s own ligand; the residues are highlighted in dark ribbon if the local structural environment (LSE) change is below a threshold value (1.0 Å). Identified hydrogen bonds are highlighted with a dashed tube (yellow) between a host base atom (tube) and a ligand atom (sphere). The driver atom and anchor atom were identified with given operational structural criteria with a GBD of 3.5 Å and LSE of 1.0 Å.