X-ray absorption measurements were performed on Ca2+ and 5 Mn2+ regenerated purple membrane in order to obtain structural information about the cation environment. For the regenerated membrane with 5 Mn2+, EXAFS analysis shows a first six-coordination sphere with two Mn-O distances (2.18 Å and 2.49 Å), whereas for the 5 Mn 2+ regenerated bleached membrane the first shell is formed by 6 oxygen atoms at 2.17 Å. In the case of Ca2+-substituted bacteriorhodopsin, ab initio calculations of the x-ray absorption cross section based on a full multiple scattering approach, with a best fit of the experimental data, show that the Ca2+ environment is composed by 6 oxygen atoms showing a distorted orthorhombic symmetry, while Ca2+ in water solution has a regular octahydrated first sphere of coordination. Our results provide strong direct evidence of the specific binding site of the metal cation in bacteriorhodopsin and are in good agreement with previous molecular models suggesting that there could be a high affinity cationic site in the proximity of the retinal pocket. © Physica Scripta 2005.