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. 2015 Oct 20;11(10):e1004551. doi: 10.1371/journal.pcbi.1004551

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© 2015 Venkatesan et al

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Fig 4 — We extracted closely spaces snapshots before and after the rotation of T308 and carried out 50 ns long simulations. (a) The RMSD of sodium 2 reflects the stability of the reinserted sodium. The time evolution of the RMSD can be classified into two groups: Large RMSD and unbinding before T308 rotation, and sodium bound to the Na2 site after rotation of T308. Panel (b) and (c) show the initial and final structure of the simulation initiated for the snapshot extracted at 160 ns. Sodium 2 was reinserted into the Na2 site and remained stable, coordinated by backbone carbonyl oxygens and the sulfur atom of the M311 side chain.