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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 3. — The PMF for the non-cognate rGTP bound RNAP complex from the on-path pre-insertion state to the insertion state and key structural measurements. (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 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, rGTP and RNA 3′ denoted is also shown.

Inline graphic — The PMF for the non-cognate rGTP bound RNAP complex from the on-path pre-insertion state to the insertion state and key structural measurements. (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 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, rGTP and RNA 3′ denoted is also shown.