The protein backbone in the area of the calcium binding site in troponin C's and muscle calcium binding parvalbumins is arranged in a helix-loop-helix where the loop region provides amino acid side chains for chelation of the cations. Although all examples of these calcium binding regions are very similar in amino acid sequence, some of the regions are low affinity calcium selective sites while others are high affinity for calcium and show magnesium competition for calcium binding. Examination of 45 examples of the calcium binding loop regions of the helx-loop-helix arrangement has enabled us to point out some important differences in the amino acid sequences. These sequence differences together with a consideration of factors affecting cation-ligand complex stability has led to the postulation of a single site model and a two site co-operative model to describe the mechanism of cation binding to a single helix-loop-helix region or to two helix-loop-helix regions related by a twofold axis of symmetry, respectively. Through the use of these models we are able to correlate the differences in amino acid sequence of the various loop regions with experimentally determined affinities for calcium and magnesium as well as predict the relative cation affinities of loop regions from the amino acid sequences.