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. 2017 Jan 13;45(6):3568–3579. doi: 10.1093/nar/gkw1351

Figure 5.

Figure 5.

Dynamics at the 7SK-motif. (A) Snapshot at 25 ns from the MD simulation started from conformation IN with U41 (pink) and U40 (cyan). (B) Inter-atomic distances, plotted along the trajectory, monitoring the base-pair A43-U66 stability (grey), the U41 motion relative to A43 (dark pink), and the U40 motion relative to C45. (C) Snapshot at 53 ns from the MD simulation started from conformation OUT, showing U41 (pink) and U40 (cyan). (D) Inter-atomic distances, plotted along the trajectory, monitoring the U40 position relative to A43. (E) Same snapshot as in (C) but showing U63 (orange) and U40 (cyan). (F) Variation of the inter-atomic distances monitoring the U63 position relative to G42 (orange) and C67 (red).