Fig. 6: The binding pocket structure and ligand binding affinities in Mg2+-free environment. | Communications Biology

Fig. 6: The binding pocket structure and ligand binding affinities in Mg2+-free environment.

From: Potential effects of metal ion induced two-state allostery on the regulatory mechanism of add adenine riboswitch

Fig. 6: The binding pocket structure and ligand binding affinities in Mg2+-free environment.The alternative text for this image may have been generated using AI.

a The snapshots of typical structures near ligand binding pocket in Kneu_bound_1. Because CJ12-P1 is almost always in a loose state in Kneu_bound_1, we have marked the important K+ ion binding site (between P1 and J23, represented by orange sphere) in this state. b The snapshots of typical structures around ligand binding pocket in Kneu_bound_2. c The contribution of each residue to the free energy (ligand binding to the AARA) in Kneu_bound_1 and Kneu_bound_2. d The contribution of each residue to the free energy is decomposed into electrostatic and non-electrostatic terms in Kneu_bound_1 and Kneu_bound_2.

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