The ionization states of the acidic residues around the Ca2+-binding sites of sarcoplasmic reticulum Ca2+ ATPase are studied by continuum electrostatic calculations and all-atom molecular dynamics simulations with explicit solvent and phospholipids. The two methods consistently indicate that Glu58 and Glu908 are protonated at neutral pH. The Ca2+ coordination and the H-bonds formed by the protonation of Glu58 and Glu908 are stable in an MD simulation, whereas the H-bonds are disrupted and the Ca2+ coordination geometry is severely altered in another simulation treating these residues unprotonated. The results clearly indicate that the H-bonds formed by protonation of Glu58 and Glu908 provide extra stability for the Ca2+-binding sites of Ca2+ ATPase.