The influence of Ca$^{2+}$ ions substitution with the rare-earth and alkali metals in the lattice of vanadate apatite (according to scheme 2Me$^{2+}$ = Ln$^{3+}$ + A$^{+}$; Ln = La, Nd, Sm, Gd, Ho; A = Li, Na, K, Rb, Cs) on the regularities of the formation of crystals’ electronic structure is studied. As established, in the case of modification with the rare-earth metals, the calcium substitution occurs preferably in Ca$_{(2)}$-position of the apatite structure, and at modifications with alkaline elements, the isomorphous substitution occurs in both crystallographic positions. The participation of the valence and subvalence atomic shells in the formation of chemical bonds is discussed, data on the participation of $4f$-electrons of rare-earth elements in formation of the structure of XPS spectra and chemical bonds with the atoms of the environment are analysed.