Extended Data Fig. 6: Conformational plasticity of the precatalytic complex.

a) Root mean square fluctuations (RMSF) of Dz^5C–RNA during MD simulations. The mean RMSF ± SEM (black area) for each nucleotide over all replicas is shown. The orange area highlights the nucleotides of the catalytic loop, and the blue areas represent nucleotides surrounding the cleavage site. b) Average structure (cartoon) from MD simulations overlaid with the structural ensemble generated from the MD trajectory (semi-transparent ribbon, with structures taken every 10 ns). c) Overlay of all seven lowest energy Dz^5C–RNA^2ʹF structures belonging to cluster I and obtained with loose-restraining in the ab initio structure calculation. In contrast to the ensembles shown in Extended Data Fig. 5, here, the loop region was excluded from structure alignment. It can be seen that the core region, including the binding arms and the orientation of the cleavage site, is reasonably well defined with an all-atom RMSD of 2.6 Å. On the contrary, the catalytic-loop region displays pronounced variations in the position within the different structures, providing an estimate of the allowed conformational space. Noteworthy, in direct comparison to the better-defined regions, the loop region does not display largely increased dynamics in the detected time regimes (Fig. 1f) and it still shows stacking interactions of the nucleotides with their neighbours, indicating locally defined conformations (Extended Data Figs. 9d and Supplementary Figure 1). In line with the MD-derived picture, it can hence be assumed that the Dz shows increased conformational plasticity in the loop region compared to the binding arm and, particularly, the cleavage-site region.