Zinc has been found in the crystal structures of inteins and the zinc ion can inhibit intein splicing both in vitro and in vivo. The interactions between metal ions and three minimized recA inteins have been studied in this work. Isothermal titration calorimetry (ITC) results show that the zinc binding affinity to three inteins is in the order of ΔI-SM > ΔΔI_hh-SM ∼ ΔΔI_hh-CM, but is much weaker than to EDTA. These data explain the reversible inhibition and the presence of zinc only in the crystal structure of ΔI-SM of recA intein. A positive correlation between binding constants and inhibition efficiency was observed upon the titration of different metal ions. Single-site binding modes were detected in all interactions, except ΔΔI_hh-CM which has two Zn sites. Zinc binding sites on ΔΔI_hh-CM were analyzed by NMR spectroscopy and ITC titration on inteins with chemical modifications. Results indicate that the Cys1 and His73 are the second zinc binding sites in ΔΔI_hh-CM. CD studies show the metal coordinations have negligible influence on protein structure. This work suggests that the mobility restriction of key residues from metal coordination is likely the key cause of metal inhibition of intein splicing.