Magnesium binding sites of the active conformation pf Hammerheadribozyme

Abstract

The modeling of the active conformation was done by using modeling program InsightII and Discover from the previous NMR, chemical modification and mutation data. This model structure has the reverse Watson-Crick GC base pair between C17 at the cleavage site and G5 at the core region. Two magnesium ions bind to this ribozyme. One binds to the pro-Rp oxygen of the P9 phosphate and the N7 nitrogen of G10.1, similarly to the crystal structure, the other to N3 of C3, the 2'O of C17 and the Sp-O of the scissile phosphate, while the Rp-O of that binds to NH2 of C3.