Fig. 7: The structural changes around ligand binding pocket and their impacts on other regions of AARA.
a The normalized distributions of RG of binding pocket for all eight simulation trajectories, and the gray dashed line corresponds to RG of binding pocket in the crystal structure (~10.6 Å). b The structure of ligand binding pocket in Mg0.3_free system (taking Mg0.3_free_1 as an example), and the hydrogen bond interactions between important residues near binding pocket are indicated by red dashed lines. An important Mg2+ ion binding site (represented by green sphere) in this state is also marked in the figure. c A schematic diagram of change in base stacking structure caused by the bending deformation of the backbone at CJ12-P1. d The change of coaxial stacking morphology between P1 and P3 caused by the deformation of CJ12-P1. The central axes of P1 (red) and P3 (blue) are drawn with the van der Waals representation of hydrogen atom. The average values and standard deviations of Opening (e) and H-rise (f) of each base pair in P1 helix for all eight simulation trajectories, and the direction of P1 (from 5’ end to binding pocket) is also shown in the figure.
