New ways to predict metal ion binding in large RNAs

Thousands of structures of RNA and DNA have been determined and are freely available in the PDB. We screen these molecules automatically and look at the exact places where metal ions occur. The metal ion binding sites are crucial for structure and function of native nucleic acids. Mapping the specific binding environments helps us to understand and predict behavior and locations of these metal ions.

Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70 000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids. The retrieved information can then be used to understand the specificity of metal ions binding to nucleic acids. In addition, comparison with other nucleic acid molecules can accelerate the process of solving new 3D structures of nucleic acids containing metals and locate metal ions more exact in the electron density map.

Group members involved: Joachim Schnabl