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. 2019 Aug 16;10:3698. doi: 10.1038/s41467-019-11627-6

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 5 — Molecular dynamics simulations of Tde-PntC (top) and Spn-LicC (bottom). a Representative conformations of the Tde-PntC active site with cognate ligand CMP-AEP and Mg²⁺ ions colored teal; non-cognate ligand CDP-Cho and Mg²⁺ ions are magenta. The transparent gray surface representation denotes the 287 Å³ cavity calculated from the crystal structure (minus CMP-AEP) using the Roll algorithm of POCASA⁴². b Representative conformations of the Spn-LicC active site showing the cognate ligand CDP-Cho and Mg²⁺ ion colored magenta; non-cognate ligand CMP-AEP and Mg²⁺ are colored teal. Transparent gray surface outlines the 381 Å³ cavity calculated from the 1JYL crystal structure coordinates after removing CDP-Cho (26). c Histogram of C4′-C5′-O5′-PA dihedral angles sampled during 10 × 150 ps independent simulations for each protein:ligand pair, using the same color scheme for each ligand (CMP-AEP = teal; CDP-Cho = magenta). Dotted lines represent crystallographically observed dihedral angles