The Cu cation binding sites of $[Cu(I){cdot}d(CpG){cdot}d(CpG)-2H]^{-1}$ complex have been investigated to explain the $[Cu{cdot}DNA]$ biological activity caused by the Cu association to DNA. The structure of $[Cu(I){cdot}d(CpG){cdot}d(CpG)-2H]^{-1}$ complex was investigated by electrospray ionization mass spectrometry (ESI-MS). The fragmentation patterns of $[Cu(I){cdot}d(CpG){cdot}d(CpG)-2H]^{-1}$ complex were analyzed by MS/MS spectra. In the MS/MS spectra of $[Cu(I){cdot}d(CpG){cdot}d(CpG)-2H]^{-1}$ complex, three fragment ions were observed with the loss of d(CpG), {d(CpG) + Cyt}, and {d(CpG) + Cyt + dR}. The Cu cation binds to d(CpG) mainly by substituting the $H^+$ of phosphate group. Simultaneously, the Cu cation prefers to bind to a guanine base rather than a cytosine base. Five possible geometries were considered in the attempt to optimize the $[Cu(I){cdot}d(CpG){cdot}d(CpG)-2H]^{-1}$ complex structure. The ab initio calculations were performed at B3LYP/6-31G(d) level.