Fig. 2: MD simulations of the input fMet–Met ribosome structural model.
a, Trajectories illustrating the evolution of the distance between the A-site Met nucleophile (Nα) and the P-site fMet carbonyl electrophile (Csp2) over 300 ns within the 30 Å RRM. b, Kernel density estimation (KDE) of the r.m.s.d. of either the C1′ nucleotides within the internal (non-fixed) 20 Å of the RRM (orange) or the Cα carbons of Met and fMet (blue) over the course of the simulation. c, Close-up of the bond-forming region of the PTC in the 2.1 Å cryo-EM model reported here (lighter shades) and a representative pose (Methods) of the simulation (darker shades) illustrating the relative positions of the Met and fMet monomers in the A and P sites, respectively. d, Radial distribution function g(r) indicates that the first and second solvation shells for the K+ and Mg2+ ions are within a distance (r) of ~4 and 6 Å of the P atoms of residues C75 and A76, respectively. e, Illustration of the Bürgi–Dunitz angle (αBD), which specifies the angle between the entering nucleophile and the Csp2=O double bond, and the Flippin–Lodge angle (αFL), which specifies the offset of the attack angle from the plane orthogonal to that defined by the carbonyl and the two adjacent substituents. σ = sigma.
