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. 2019 Mar 27;47(9):4721–4735. doi: 10.1093/nar/gkz213

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© The Author(s) 2019. 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 6. — The constructed PMF for the non-cognate dATP bound structure from the pre-insertion on-path to the insertion state and key structure measures. (A) The PMF obtained from the umbrella sampling simulations along the collective reaction coordinate . (B) The O-helix angle obtained from the five windows labeled on the PMF curve. (C) The distance distribution between Y639 and RNA3′-2OH. (D) The five representative structures along the reaction coordinate (in stereo views). A pre-insertion configuration (config 1) with TN(i), Y639, O-helix, MgA/B, dATP and RNA 3′ denoted is also shown. The black dashed circle highlights the two magnesium ions (MgA and MgB) that switch roles in stay and leave.

Inline graphic — The constructed PMF for the non-cognate dATP bound structure from the pre-insertion on-path to the insertion state and key structure measures. (A) The PMF obtained from the umbrella sampling simulations along the collective reaction coordinate . (B) The O-helix angle obtained from the five windows labeled on the PMF curve. (C) The distance distribution between Y639 and RNA3′-2OH. (D) The five representative structures along the reaction coordinate (in stereo views). A pre-insertion configuration (config 1) with TN(i), Y639, O-helix, MgA/B, dATP and RNA 3′ denoted is also shown. The black dashed circle highlights the two magnesium ions (MgA and MgB) that switch roles in stay and leave.