Precatalytic state and position of the reactants for group II intron splicing. The structure of the precatalytic state in the presence of Ca2+/K+ (4FAQ, ) allows the identification of all essential reactive elements. The active site scaffold (green cartoon representation) is composed of highly conserved motifs (J2/3 junction, catalytic triad, two-nucleotide bulge). The intron 5′-end connects to the 5′-exon (blue cartoon representation) via the scissile phosphate (orange sphere) and forms the 5′-splice junction. The base-paired helical structure formed by the intron and the exon binding sites (IBS1, EBS1) determines the fidelity of splicing. Finally, a four-metal heteronuclear center formed by Mg2+ ions (M1-M2, yellow spheres) and K+ ions (K1-K2, violet spheres) promotes catalysis, by correctly orienting and activating the reacting groups, including a water molecule (cyan sphere) that acts as the putative nucleophile in the reaction.