Molecular dynamics simulations in the presence and absence of Sr. A. A comparison between the Pex5p(C) structures along the simulation trajectories. The difference between the simulation in the presence and absence of the Sr2+ ion is plotted as a function of running time. B. Superposition of the new apo structure (blue) with the old apo structure (cyan), the SCP2-loaded structure (yellow), and the simulation end-states in the presence (green) and absence (orange) of the Sr2+ ion. Residues 503–639 were used for the superposition to highlight the orientation between the N- and C-terminal halves. The tail of SCP2 enters the binding cavity from below (yellow ribbon). Note the similarity between the liganded structure and the simulation without Sr2+. An animated presentation of the result can be found in the additional data file 2.