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. 2022 Jan 26;23(3):1420. doi: 10.3390/ijms23031420

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© 2022 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).

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Dynamics of the sodium ion. (A) H₁R structure (white ribbons) depicting the Na+ position (blue spheres) derived from simulation at time intervals of 1 ns. (B) The Na+ ion can adopt different positions in the binding pocket while still remaining attached to D73^2.50. (C) Distance between D73^2.50 and the sodium ion for all simulations that contained a sodium ion. H₁R-DS (run1, run2), H₁R-DSP (run3, run4) and H₁R-S (run9, run10). (D–G) Frames from the H₁R-DS (run2) simulation at 0 ns, 100 ns, 1000 ns and 1700 ns. Sodium is depicted as a blue sphere, interacting residues are shown in cyan and the ligand doxepin is highlighted by green highlighted carbon atoms. The receptor is shown as a white ribbon.