Experiments affecting calcium signaling often lead to changes in the calcium transient height. The present work is designed to approach this effect theoretically. Use of computational model let us to follow results of precisely designed changes in the endoplasmic reticulum distribution as a possible cause of cytoplasmic free calcium ion level. Obtained results suggest that indeed, rearrangement of the endoplasmic reticulum elements may be responsible for modulation of calcium signal's strength. We have also noticed that even if the endoplasmic reticulum concentration levels are local, the resulting changes in free calcium concentration are global and evenly distributed throughout the cell. The used mathematical method proved to be a powerful tool which made us understand the chemical dynamics of nonequilibrium processes of calcium transient formation. Presented data show how Ca2+ signal resulting from IP3 provoked release of calcium from the endoplasmic reticulum may depend on the cytoskeleton structure.