Plastocyanin was the first of the blue copper proteins to be characterised by X-ray crystallography. It features an eight-stranded antiparallel β-barrel containing one copper center.
Structures of the protein from poplar, algae, parsley, spinach, and French bean plants have been characterized crystallographically.  In all cases the binding site is generally conserved. Bound to the copper center are four ligands: the imidazole groups of  two histidine residues (His37 and His87), the thiolate of Cys84 and the thioether of Met92. The geometry of the copper binding site is described as a ‘distorted trigonal pyramidal’.  The Cu-S (cys) contact is much shorter (207 picometers) than Cu-S (met) (282 pm) bond.  The elongated Cu-thioether bond appears to destabilise the Cu state thereby enhancing its oxidizing power. The blue colour (597 nm peak absorption) is assigned to a charge transfer transition from S to Cu-y</sub>.
In the reduced form of plastocyanin, His-87 becomes protonated.
While the molecular surface of the protein near the copper binding site varies slightly, all plastocyanins have a hydrophobic surface surrounding the exposed histidine of the copper binding site.  In plant plastocyanins, acidic residues are located on either side of the highly conserved tyrosine-83.  Algal plastocyanins, and those from vascular plants in the family Apiaceae, contain similar acidic residues but are shaped differently from those of plant plastocyanins—they lack residues 57 and 58.  In cyanobacteria, the distribution of charged residues on the surface is different from eukaryotic plastocyanins and variations among different bacterial species is large. Many cyanobacterial plastocyanins have 107 amino acids. Although the acidic patches are not conserved in bacteria, the hydrophobic patch is always present.  These hydrophobic and acidic patches are believed to be the recognition/binding sites for the other proteins involved in electron transfer.