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. 2018 Sep 20;46(19):9960–9970. doi: 10.1093/nar/gky833

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© The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 5. — Hydrogen bonds created by aminoglycoside 6′ group. (A) The percentage of frames in which the most frequent contacts with either riboswitch atoms or water molecules are present during last 50 ns of trajectories. Only contacts occurring in more than 5% of frames in any simulation are shown. (B, C) Frequent hydrogen bonds between RIO or PAR and RNA in REMD simulations. The distances shown in Å are measured between non-hydrogen atoms in the cluster representative structures. The inset shows the second most common contact of PAR 6′-OH group, namely with U10:O4 (see A). (D, E) The same site in NMR structures (PDB IDs 2mxs and 2n0j).