MINAS

MINAS provides a database of metal ions associated with nucleic acids (DNA and RNA) to enable analysis of metal ion coordination environments and their roles in nucleic acid folding, stability, and catalysis.

Key Features:

• Database content: Contains data on over 70,000 metal ions from 36 elements observed in more than 2,000 nucleic acid structures.
• Data sources: Structures and metal-ion annotations are sourced from the Protein Data Bank (PDB) and the Nucleic Acid Database (NDB).
• Coordination environment analysis: Provides innersphere, outersphere, and larger coordination-context descriptions for metal ions.
• Metal-ligand metrics: Reports metal-ligand distances and identifies ligands by element or functional group and by residue.
• Experimental metadata: Associates metal-ion observations with experimental methods and PDB entry–related information.
• Searchable attributes: Enables queries by metal ion type, metal-ligand distances, ligands, residues, experimental method, and PDB entry metadata.
• Data export (miniPDB): Exports miniPDB files containing the metal ion and its coordination environment within a 15 Å radius for binding-pocket analysis.
• Updates: Incorporates new structures on a monthly update cycle.

Scientific Applications:

• Structural analysis of nucleic acids: Comparative and detailed analysis of metal-binding sites across DNA and RNA structures.
• Study of folding and stability: Investigation of how metal ions contribute to nucleic acid folding and structural integrity.
• Catalysis and ribozyme research: Examination of metal-ion roles in catalytic mechanisms, including ribozymes, via coordination geometries and ligand interactions.
• Binding-pocket characterization: Identification and structural characterization of metal-binding pockets using extracted coordination environments.

Methodology:

Metal-ion data are extracted from PDB and NDB entries; coordination environments are classified into innersphere, outersphere, and larger contexts; metal-ligand distances and ligand identities (element or functional group, residues) are computed; miniPDB files are generated to include the metal ion and surrounding atoms within a 15 Å radius.