We present the tandem mass spectrometry applications carried out to elucidate the coordination structure of Zn(II) bound lysine ternary complexes, $(Zn+Lys+Lys-H)^+$, which is a good model system to represent a simple (metallo)enzyme-substrate complex (ES). In particular, experimental efforts were focused on revealing the involvement of a lysine side chain ${varepsilon}$-amino group in the coordination of $Zn^{2+}$ divalent ions. MS/MS fragmentation pattern showed that all the oxygen species within a complex fell off in the form of $H_2O$ in contrast to those of other ternary complexes containing amino acids with simple side chains (4-coordinate geometries, Figure 1a), suggesting that the lysine complexes have different coordination structures from the others. The participation of a lysine basic side chain in the coordination of Zn(II) was experimentally evidenced in MS/MS for $N{varepsilon}$-Acetyl-L-Lys Zn(II) complexes with acetyl protection groups as well as in MS/MS for the ternary complexes with one $NH_3$ loss, $(Zn+Lys+Lys-NH_3-H)^+$. Detailed structures were predicted using ab initio calculations on $(Zn+Lys+Lys-H)^+$ isomers with 4-, 5-, and 6-coordinate structures. A zwitterionic 4-coordinate complex (Figure 7d) and a 5-coordinate structure with distorted bipyramidal geometry (Figure 7b) are found to be most plausible in terms of energy stability and compatibility with the experimental observations, respectively.