Figure 4. The Mn²⁺-free E. coli yybp-ykoY aptamer crystal structure.

A) Overall superposition of the E. coli Mn²⁺-free molecule B (blue) and L. lactis Mn²⁺-bound (gray) aptamer structures. The shifted L3 loop of the E. coli structure is in cyan. B) Secondary structure of the E. coli crystal structure, numbered according to wild-type sequence. C) Binding site close-up of the E. coli (teal) and L. lactis (gray) L3 loops. The L. lactis M_A and M_B are shown in cyan and bright pink. Two Sr²⁺ ions from the E. coli structure, one at M_A and one in a new site, are shown in green. The phosphoryl oxygens in the E. coli Mn²⁺-free structure equivalent to those that bind M_B in the L. lactis Mn²⁺-bound structure are shown as enlarged red spheres. The M_A binding site is circled in yellow.