Mg2+ ions: do they bind to nucleobase nitrogens?

Area of Science:

• Structural Biology
• Biochemistry
• Molecular Biophysics

Background:

• Magnesium ions (Mg2+) play crucial roles in nucleic acid structure and function.
• Accurate determination of Mg2+ binding modes is essential for understanding these roles.
• Purine N7 atoms are often proposed as key binding sites for divalent metal ions.

Purpose of the Study:

• To survey the Protein Data Bank (PDB) for Mg2+ inner-sphere binding patterns to nucleobase imine atoms.
• To clarify the actual binding sites of Mg2+ in nucleic acid structures.
• To provide guidelines for accurate ion assignment in structural studies.

Main Methods:

• Survey of the Protein Data Bank (PDB) for Mg2+ binding sites.
• Analysis of electron density patterns in crystallographic and cryo-electron microscopy (cryo-EM) data.
• Comparison of Mg2+ binding with other divalent metal ions (Mn2+, Zn2+, Cd2+).

Main Results:

• Mg2+ ions are frequently misidentified near nucleobase imine nitrogens, often being Na+, K+, NH4+, water, or artifacts.
• Mg2+ ions generally do not bind to purine N7 atoms, contrary to previous assumptions.
• Other divalent ions like Mn2+, Zn2+, and Cd2+ can bind to N7 atoms due to higher affinity.
• A novel Zn2+ binding site involving two purine N7 atoms in a ribosomal context was identified.

Conclusions:

• The proposed Mg2+ binding to N7 atoms in nucleic acids is largely based on misinterpretations of structural data.
• Accurate ion assignment is critical for understanding Mg2+ roles in nucleic acid function and catalysis.
• Guidelines are provided to improve Mg2+ assignment in structural biology techniques.
• Findings impact the interpretation of ion substitution experiments and mechanistic studies of ribozymes.