Structural changes of the PrBa2Cu3O7 compound as Cu are partially replaced by Ga or Zn are studied by using high resolution neutron diffraction measurements. Rietveld method is followed in refining the diffraction patterns. Ga atom is found to enter the Cu site in the CuO-chain layers, that also causes the O in that layer to become disorder with equal probability to occupy the sites along the a and along the b axis directions. This effectively destroys the Cu-O chain ordering observed in the undoped system, and results in (Cu/Ga)-O chains run in both the a and b axis directions. Tetragonal symmetry for the Ga-doped compound is resulted. Zn atom, on the other hand, replaces the Cu in the CuO2-plane layer, which make no significant effect on the basic structure except a small oxygen disorder in the chain layers. The bond lengths of Pr and the O in the CuO2-plane layers increase slightly in the Ga-doped system, whereas that in the Zn-doped system remains basically unaffected.