Techniques, tools and best practices for ligand electron-density analysis and results from their application to deposited crystal structures

The potential causes of severe misinterpretation of ligand electron density in a surprisingly large number of protein-ligand structure complexes are analyzed. Techniques and tools are presented together with suggestions for good practice aimed at minimizing overinterpretation and mistakes in protein-ligand structure models.

Structure of human apurinic/apyrimidinic endonuclease 1 with the essential Mg²⁺ cofactor

Human AP endonuclease 1 (APE1) belongs to the DNase I-like superfamily of enzymes that require divalent cation(s) to catalyze phosphoryl-transfer reactions. A new 1.92 Å resolution crystal structure of APE1 reveals ideal octahedral coordination of a single Mg²⁺ ion and informs on the role of this essential cofactor.