FIGURE 3.

Loop E dynamics. Root mean square deviations (RMSd) and selected H-bond distances along the trajectories. (a) and (b): RMSd of the simulated structures with respect to the starting geometries. The “Ebac refold with Mg²⁺” trajectory RMSd is calculated with respect to the crystal geometry and will be discussed later. RMSd for the Echl sequence is slightly increased by unoptimized initial geometries of three substituted basepairs. (c) EbacNa1 simulation: the U77/A99 basepair exhibited two major opening events (at 2.6–4.3 ns and 4.8–7.7 ns) while the symmetry-related A73/U103 was entirely stable. (d) EchlMg simulation: opening event of A76-A100 basepair correlated with release of Mg4 at 4.3 ns and major changes of the deep groove (see the text for further details).