The role of the C-domain sites of cardiac troponin C in the modulation of the calcium signal remains unclear. In this study, we investigated the effects of hypertrophic cardiomyopathy-linked mutations A8V, E134D, and D145E in cardiac troponin C on the properties of the C-domain sites. The A8V mutation had essentially no effect on the calcium or magnesium binding properties of the C-domain sites, while the mutation E134D moderately decreased calcium and magnesium binding affinities. On the other hand, the D145E mutation affected cooperative interactions between sites III and IV, significantly reducing the calcium binding affinity of both sites. Binding of the anchoring region of cardiac troponin I (corresponding to residues 34-71) to cardiac troponin C with the D145E mutation was not able to recover normal calcium binding to the C-domain. Experiments utilizing the fluorescent hydrophobic probe bis-ANS suggest that the D145E mutation dramatically reduced the extent of calcium-induced hydrophobic exposure by the C-domain. At high nonphysiological calcium concentration, A8V, E134D, and D145E mutations minimally affected the affinity of cardiac troponin C for the regulatory region of cardiac troponin I (corresponding to residues 128-180). In contrast, at lower physiological calcium concentration, the D145E mutation led to an approximately 8-fold decrease in the affinity of cardiac troponin C for the regulatory region of cardiac troponin I. Our results suggest that calcium binding properties of the C-domain sites might be important for the proper regulatory function of cardiac troponin C.