Figure 3

Preferred positions of multivalent ions in long equilibrium simulations. (a–c) Space occupied by Ca²⁺ during C5 (a), Ba²⁺ during B2 (b) and Gd³⁺ during G2 (c) 110 ns-long trajectories are shown as green, peach, and magenta meshes, respectively. (e–f) Ion distributions in the C5, B2 and G2 simulations respectively in 2D coordinates: the distance along z-axis illustrated in Fig. 2a and the polar angle in a plane perpendicular to the pore axis at z = 0. Red, green, blue, and yellow histograms represent individual ions positioned at the recruitment sites. Black and magenta histograms represent two ions located elsewhere in the channel vestibule. Orange and cyan histograms represent two ions located at the pore sites. Red dashed lines indicate ion binding sites predicted by crystal structures at D541 (Site 1), T538 (Site 2), and M569 (Site 3).