Figure 2.

A three-channel scheme describing the Mg²⁺-dependent and independent pathways for HDV ribozyme catalysis. In 1 M NaCl in the absence of Mg²⁺, the ribozyme reacts at a basal rate with rate constant k₁ (channel 1). Increasing concentrations of Mg²⁺ accelerate this rate in a log-linear fashion (channel 2) up to a point, after which the rate becomes independent of Mg²⁺ concentration (channel 3). The Mg²⁺ ion associated with channel 2 conditions is thought to be primarily structural, binding via inner sphere coordination to a base quadruple involving a protonated C41. Under channel 3 conditions, a second, catalytic, Mg²⁺ ion binds via outer sphere coordination in the vicinity of the active site. This fully hydrated Mg²⁺ ion is thought to participate in general acid-base catalysis. [Adapted from (10).]