Fig. 1: The structure of add adenine riboswitch and the geometry of ligand binding pocket. | Communications Biology

Fig. 1: The structure of add adenine riboswitch and the geometry of ligand binding pocket.

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

Fig. 1: The structure of add adenine riboswitch and the geometry of ligand binding pocket.The alternative text for this image may have been generated using AI.

a The tertiary structure of add adenine riboswitch in a complex with the adenine (ADE) ligand generated using VMD. The adenine ligand is depicted with a van der Waals representation, and each part of riboswitch is marked with different colors. b The secondary structure of add adenine riboswitch, which is marked similarly to the tertiary structure. The tertiary interactions are indicated with the notation of the Leontis–Westhof–Zirbel method87. For the purpose of clarity, several unimportant tertiary contacts are not shown. c Chemical structure of adenine molecule (nitrogenous groups are identified in light blue). d The top and top-side views of ligand binding pocket. The hydrogen bonds are indicated by red dashed lines (top view), and the base stacking information in the binding pocket is shown in top-side view.

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