Fig 2. Atomic fluctuations calculated from MD simulations.

A, B: Mean (± SEM) atomic fluctuations (RMSF) on a per nucleotide level for Gsw^apt (A) and Gsw^loop (B) over the three simulations for each system setup. Secondary structure regions are depicted above the plots and colored according to Fig 1A. Red: simulations in the absence of Mg²⁺ ions; green: simulations with 12 Mg²⁺ ions per RNA molecule; blue: simulations with 20 Mg²⁺ ions per RNA molecule. C, D, E: Differences in atomic fluctuations projected onto the RNA structure. Larger differences are colored red, smaller differences blue. Nucleotides responsible for ligand binding are shown as sticks. C: Difference in atomic fluctuations for Gsw^apt of 0 Mg²⁺—20 Mg²⁺ ions per RNA molecule. D: Difference in atomic fluctuations in the absence of Mg²⁺ for Gsw^loop—Gsw^apt. E: Difference in atomic fluctuations for Gsw^loop of 0 Mg²⁺—20 Mg²⁺ ions per RNA molecule.