The electronic structures of the perturbed blue copper proteins stellacyanin (STC) and cucumber basic protein (CBP, also called plantacyanin, PNC) are defined relative to that of the well-understood "classic" site found in plastocyanin (PLC) by combining the results of low-temperature optical absorption, circular dichroism, and magnetic circular dichroism spectra with density functional calculations. Additionally, absorption and magnetic circular dichroism spectra of Alcaligenes denitrificans wild-type and M121Q azurin are presented and compared to PLC and STC, respectively. These studies show that the principal electronic structure changes in CBP/PNC, with respect to PLC, are a small shift of the ligand field transitions to higher energy and a rotation of the Cu d(x2-y2) half-filled HOMO which increases the pseudo-sigma and decreases the pi interactions of the cysteine (Cys) sulfur with Cu d(x2-y2) and, in addition, mixes some methionine (Met) sulfur character into the HOMO. The geometrical distortion responsible for the perturbed electronic structure, relative to PLC, involves a coupled angular movement of the Cys and Met residues toward a more flattened tetragonal structure. In contrast to CBP/PNC, STC (which has the axial Met substituted by Gin) has its ligand field transitions shifted to lower energy and undergoes much smaller degrees of HOMO rotation and Cys pseudo-sigma/pi mixing; no axial glutamine character is displayed in the HOMO. These changes indicate a tetrahedral distortion in STC. Therefore, perturbed spectral features are consistent with both tetragonal and tetrahedral geometric distortions relative to PLC. These perturbations are discussed in terms of the increased axial ligand strength in these proteins (i.e., short Cu-S(Met) in CBP/PNC and O epsilon(Gln) in STC). This induces an similar to epsilon(u)-like distorting force which either results in a tetragonal distortion of the site (CBP/PNC) or is structurally restrained by the protein (STC and M121Q).