Fig. 3

Structural dynamics of inner-shell ligands of the M_A,Mg and M_B,Mn sites, L3 and L1 loops as revealed by MD simulations. a The population of native inner-shell contacts in the M_A,Mg and M_B,Mn sites in percent as a function of the type of ion in these sites. A representative structure of the b M_A,Mg and c M_B,Mn site as typically observed in MD simulations with a K⁺ ion occupying the site. The most labile inner-shell contacts are depicted in cyan. d 2D representation of the most stable part of the L1–L3 tertiary interaction that is likely anchored by the A-minor interaction and related A10|A46 stacking. e Partial unfolding of the stacking pattern in the L3 loop observed upon replacement of Mn²⁺ with K⁺ in the M_B,Mn site. f The loss of native G9–G93 trans Watson-Crick/Hoogsteen and G8–A94 trans Sugar-Edge/Hoogsteen base pairing, and g loss of the S-turn backbone conformation involving a phosphate notch forming part of the M_A,Mg ion binding site in response to loss of the L1–L3 tertiary interaction with its A10…G66 = C44 A-minor interaction