Chronic hepatitis B virus (HBV) infection is a major cause of hepatocellular carcinoma (HCC) worldwide. The pre-S2 mutant large HBV surface (Delta2 LHBS) protein, which contains an in-frame deletion of approximately 17 amino acids in LHBS, is highly associated with risks and prognoses of HBV-induced HCC. It was previously reported that Delta2 LHBS interacts with the Jun activation domain-binding protein 1 (JAB1), a zinc metalloprotease. This promotes the degradation of the cell cycle regulator p27Kip1, and is believed to be the major mechanism for Delta2 LHBS-induced HCC. In this study it was found that the interaction between JAB1 and Delta2 LHBS is facilitated by divalent metal Zn2+ ions. The binding of JAB1 to Delta2 LHBS requires the JAB1/CSN5 MPN metalloenzyme (JAMM) motif and residue H138 that binds to Zn2+ ions in JAB1. Isothermal titration calorimetry showed that Delta2 LHBS binds directly to Zn2+ ions in a two-site binding mode. Residues H71 and H116 in Delta2 LHBS, which also contact Zn2+ ions, are too indispensable for Delta2 LHBS-mediated p27Kip1 degradation in human HuH7 cells. These results suggest that developing drugs that interrupt interactions between Delta2 LHBS and JAB1 can be potentially used to mitigate Delta2 LHBS-associated risks for HCC.