Employing detailed atomistic modeling we elucidate the mechanisms behind ion-binding to proteins and other bio-molecules and conclude that (1) small, hard ions bind via direct ion-pairing to charged surface groups and (2) large, soft ions bind to non-polar groups via a solvent assisted attraction. Our predictions are in qualitative agreement with bulk electrolyte data and may provide an important clue for the basic understanding of ion-specific effects in biological systems.