Fig 3. Rigidity analyses.

A: Nucleotides involved in binding guanine in the binding site of the aptamer domain of Gsw (PDB ID 1Y27 [26]). Black dashed lines indicate hydrogen bonds. B: Constraints (black lines) added to conformations of the apo aptamer domain of Gsw to model the presence of guanine in the binding site for rigidity analyses. C, D, E, F: Nucleotide-wise differences in the probability to be in the largest rigid cluster (Δp_lrc(i), Eq 1, E_HB = −0.6 kcal/mol for the rigidity analyses) between the ligand being present or absent in the aptamer domain, projected onto the aptamer domain of Gsw^apt (C, E) and Gsw^loop (D, F) in the absence of Mg²⁺ ions (C, D) and in the presence of 20 Mg²⁺ ions (E, F).