Many bioactive compounds are O-glycosylated metabolites; however, the hydrolytic sensitivity of O-glycosidic linkage limits their therapeutic applications. Enzymatically and chemically stable C-glycosidic bonds are thought of as a potential solution to overcome this problem, although the insufficient information about the structural preferences and interactions that distinguish the C- from the O-glycosylation reactions has hindered the development of enzyme engineering strategies. Thus, in this work, the O-glycosyltransferase LanGT2 (O-LanGT2) and its engineered C-C bond-forming variant (C-LanGT2), which catalyze the initial glycosylation step in the biosynthesis of the antibiotic landomycin A, were studied by means of all-atom Molecular Dynamics simulations. Our results indicate that precise positioning of the acceptor substrate tetrangulol (TET) seems to be determined by the flexibility of the loop 51-62, which gives rise to slightly different secondary structural elements that modulate the interactions between this loop and TET. In O-LanGT2, the most notable interactions between TET and the loop 51-62 involve R59 and A62, whereas in C-LanGT2 they involve A8, I58, and I62. Although A8 is not part of the loop 51-62, it turns out to be key to the binding mode exhibited by TET in C-LanGT2. Thus, the TET-A62 (O-LanGT2) and TET-A8 (C-LanGT2) interactions appear to be critical to accomplish the O- and the C-glycosidic bond specificity, respectively. Finally, all results together shed light on the molecular basis governing the O- and C-bond specificity, revealing that the underlying molecular mechanism that tunes the orientation of TET at its binding pocket involves hydrophobic interactions.