Preferential chelation of cationic ligands to axial-equatorial oxygens over equatorial-equatorial dianionic oxygens: implication to the mechanism of action of ribozymes.

Effects of chelation of H2O, H+, and Mg2+ to two kinds of potential pentacoordinate intermediates of ribozyme reactions were investigated by ab initio molecular orbital calculations. Unexpectedly, in all cases examined, axial-equatorial chelations were found to be more stabilizing than equatorial-equatorial chelations. These results support the hypothesis that Mg2+ ion is bound to the equatorial phosphoryl oxygen and the axial leaving/attacking oxygen in the transition state of ribozyme reactions.