The figure displays a metal coordination site shared by Lysyl oxidase from Pichia pastoris (1w7c, left) and rabbit glycogenin-1 (1ll2, right). These proteins belong to the Supersandwich and Nucleotide-diphospho-sugar transferases folds respectively. The structural match includes three residues with an RMSD of 0.48 Å.

The representation using the C-alpha and the geometric centroid of the side chain is well-suited to a case like this since metal binding sites usually have a fixed geometry and are composed of specific aminoacid types. Moreover it allows to include side-chain information without increasing the computational cost, because residues are still paired as single entities, i.e. the points used to represent them are not treated independently.