Large ribozymes require divalent metal ions to fold. We show here that
the tertiary structure of the Tetrahymena group I intron P4-P6 domain
nucleates around a magnesium ion core. In the domain crystal structur
e, five magnesium ions bind in a three-helix junction at the centre of
the molecule. Single atom changes in any one of four magnesium sites
in this three-helix junction destroy folding of the entire 160-nucleot
ide P4-P6 domain. The magnesium ion core may be the RNA counterpart to
the protein hydrophobic core, burying parts of the RNA molecule in th
e native structure.