Fig. 5: Diffuse cryo-EM densities and molecular dynamics water networks.

Comparison of density features surrounding the RNA (red) between the cryo-EM maps and molecular dynamics. The first column labels the nucleotides in the region, coloured according to domains from Fig. 1. The second and third columns are the 2.2 Å and 2.3 Å cryo-EM densities, respectively, at 3σ at least 1.8 Å away from the RNA coloured in transparent green (within 2.5 Å of a Mg²⁺ ion) and red (remainder of density). The models are displayed in white, with the SWIM modelled Mg²⁺ ion as green spheres and water as red spheres. The final column is the predicted density from molecular dynamics after local alignment (Methods). Water (dark red at 101 M, light red at 68 M), Mg²⁺ ion (dark green at 46 M, light green at 14 M) and Na⁺ ion (dark purple at 28 M, light purple at 14 M) densities are displayed. The 2.2 Å RNA is pictured in white for reference. a, Densities of water and ions around the RNA for a global view of the ribozyme. b–f, Specific regions of interest, showing water networks along the groove of helices and around the backbone (b), a network of waters around the backbone of P6a (c), water networks surrounding the catalytic core (d,e) and a water wire bridging the backbone of two RNA helices (f). The black circle (c) highlights a density feature in cryo-EM and molecular dynamics simulations whose irregular shape precluded SWIM assignment of an atomically ordered water. A density of unknown identity in the binding site for the guanine substrate is circled in black (d,e). See Supplementary Video 2 to visualize the 3D context of panels b–e.