Topological insulators are characterized by the existence of band inversion and the possibility of the realization of surface states. Doping with a magnetic atom, which is a source of the time-reversal symmetry breaking, can lead to realization of novel magneto-electronic properties of the system. In this paper, we study effects of substitution by the transition metal ions (Mn, Fe, Co and Ni) into Bi2Se3 on its electric properties. Using the ab inito supercell technique, we investigate the density of states and the projected band structure. Under such substitution the shift of the Fermi level is observed. We find the existence of nearly dispersionless bands around the Fermi level associated with substituted atoms, especially, in the case of the Co and Ni. Additionally, we discuss the modification of the electron localization function as well as charge and spin redistribution in the system. Our study shows a strong influence of the transition metal-Se bond on local modifications of the physical properties. The results are also discussed in the context of the interplay between energy levels of the magnetic impurities and topological surface states.