This study explores the structural properties and energy landscapes of the physiologically important bis(
l
‐asparaginato)copper(II) [Cu(
l
‐Asn)
2
] and (
l
‐histidinato)(
l
‐asparaginato)copper(II) [Cu(
l
‐His)(
l
‐Asn)]. The conformational analyses in the gas phase and implicitly modeled water medium, and magnetic parameters of electron paramagnetic resonance spectra were attained using density functional theory calculations. The apical Cu
II
coordination and hydrogen bonding were analyzed. Predicted lower‐energy structures enabled the confirmation and, for apical bonding, also the refinement of structural proposals from literature. Available experimental results were indecisive regarding the amido‐group binding in the Cu
II
equatorial plane in solutions, but the examination of the relative stability of Cu(
l
‐Asn)
2
conformers in 30 binding modes confirms the glycine‐like mode as the most stable one. Previously reported experimental results for Cu(
l
‐His)(
l
‐Asn) were interpreted for
l
‐His to have a tridentate histamine‐like mode. However, the aqueous conformers with
l
‐His in the glycinato mode are also predicted to have low energies, which does not contradict the tridentate
l
‐His binding. The predicted magnetic parameters of conformers with an apical oxygen atom (intramolecular or from a water molecule) can reproduce the experimental data. An extent of conformational flexibility and abundance of
l
‐His‐containing ternary copper(II) amino acid complexes under physiological conditions may be related.