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Location of two binding sites for sodium ions (red/gray spheres) with a long associated residence time (>1 ns) during the simulation of the closed kt38 structure (reaction coordinate distance δ = 6 Å). The second A-minor interaction (atom color code) and the backbone (orange/gray) are in bold stick representation. Bases C936, C937, G938, C1033, and G1034, which contact the ions at the two binding sites, are also atom-color coded (thin sticks).
