Fig. 2
From: Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch
Conformational differences in the metal ion binding sites and B-factors in the structures. Close-up view of the MA,Mg (black) and MB,Mn (purple) metal ion binding sites of a Conformer 1 and b Conformer 2 showing different contacts with surrounding L1 and L3 residues. Waters are shown as red spheres. The lost metal ion contacts are shown as red dashed lines with their distances. The anomalous difference map at 4σ (magenta mesh) shows that Sr2+ is not observed in Conformer 1 and weakly occupies the MA,Mg site but not the MB,Mn site in Conformer 2. The Llac-Mn structure is shown in Supplemental Fig. 5 in the same orientation for comparison. Overall X. oryzae Conformer 1 (c) and Conformer 2 (d) structures, colored by individual atomic temperature B-factors (range: 38–135 Å2 for Conformer 1, 44–170 Å2 for Conformer 2). Notice both are well-structured in L1 and in P3 around the binding site. However, Conformer 1 is much more tightly structured in L3 than is Conformer 2. Also, the metal ions in Conformer 1 are somewhat less variable. In both molecules, there is flexibility around the 4WJ
