New hexadentate nickel(II) complex Mg[Ni(1,3-pd3ap)]·10H2O containing unsymmetrical edta-type ligand, 1,3-propanediamine-N,N,N′-triacetate-N′-3-propionate (1,3-pd3ap), has been prepared, chromatographically separated, and characterized. Only one [trans(O5)] of the two possible geometrical isomers was isolated. In this isomer, the two five-membered glycinate rings (R rings) occupy trans-axial sites while the one glycinate ring and one β-alaninate ring lie in the equatorial plane with the two diamine nitrogens (G rings). This result confirms the assignment made on the basis of the density functional theory (DFT), IR, and UV–Vis spectral data analysis. In order to see cation influence on the structural and electronic behavior, [Ni(H2O)6][Ni(1,3-pdta)]·2H2O complex has also been prepared and its structure verified by an X-ray analysis. Spectral data and electronic transition assignment, DFT–natural bonding orbital, and an extensive strain analysis are discussed in comparison with those of other [Ni(edta-type)]2− complexes of known configuration.