Structural biology of the lanthanides—mining rare earths in the Protein Data Bank

• We examine the coordination chemistry of the lanthanides in protein structures.
• The coordination numbers in the first coordination sphere are very variable.
• The coordination numbers resemble those that are observed in small molecules or in water solution.
• The coordination polyhedra are very variable.
• Lanthanides are frequently observed in packing bridges between symmetry equivalent molecules.

With its about 100,000 three-dimensional structures, the Protein Data Bank is a copious source of information: it contains also some hundreds of structures of macromolecules complexed with lanthanide cations, which are examined here. These cations, which are found in a wide variety of protein types, were introduced to determine the structures, by exploiting their anomalous dispersion (in crystallographic studies, where they are also used as crystallization additives) or the paramagnetic pseudocontact shifts (in NMR analyses). The coordination numbers in the first coordination sphere are very variable, though they tend to be close to those that are observed in small molecules or in water solution. The coordination polyhedra are also quite variable as it can be expected for large cations. Interestingly, lanthanide cations are frequently observed in packing bridges between symmetry equivalent molecules in crystals, where they tend to form polynuclear complexes, with up to seven cations bridged by water/hydroxide ligands.

The protein crystal structures of the Protein Data Bank that contains lanthanide cations are inspected to determine the importance of lanthanides in crystallization and structure determination. Moreover, the lanthanide coordination numbers and geometries are scrutinized together with the packing bridges determined by the lanthanides.Figure optionsDownload as PowerPoint slide