Assessing the Potential Effects of Active Site Mg2+ Ions in the glmS Ribozyme-Cofactor Complex

Sixue Zhang, David R. Stevens, Puja Goyal, Jamie L. Bingaman, Philip C. Bevilacqua, Sharon Hammes-Schiffer

Research output: Contribution to journalArticlepeer-review


Ribozymes employ diverse catalytic strategies in their self-cleavage mechanisms, including the use of divalent metal ions. This work explores the effects of Mg2+ ions in the active site of the glmS ribozyme-GlcN6P cofactor complex using computational methods. Deleterious and potentially beneficial effects of an active site Mg2+ ion on the self-cleavage reaction were identified. The presence of a Mg2+ ion near the scissile phosphate oxygen atoms at the cleavage site was determined to be deleterious, and thereby anticatalytic, due to electrostatic repulsion of the cofactor, disruption of key hydrogen-bonding interactions, and obstruction of nucleophilic attack. On the other hand, the presence of a Mg2+ ion at another position in the active site, the Hoogsteen face of the putative base, was found to avoid these deleterious effects and to be potentially catalytically favorable owing to the stabilization of negative charge and pKa shifting of the guanine base.

Original languageEnglish (US)
Pages (from-to)3984-3988
Number of pages5
JournalJournal of Physical Chemistry Letters
Issue number19
StatePublished - Oct 6 2016

ASJC Scopus subject areas

  • General Materials Science
  • Physical and Theoretical Chemistry


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