Only beta-NGF, the subunit of the 7S NGF complex, exhibits NGF activity, but the function of the zinc ion in native beta-NGF has received little attention. Flameless atomic absorption spectroscopy (FAAS) measurements reveal that native beta-NGF contains Zn(II) with a Zn(II)/beta-NGF stoichiometry of 1:14.6. The presence of Zn(II) in the native molecule results in significant changes of the secondary structure and local tertiary structure around Trp(s) with respect to those of apo beta-NGF, as suggested by spectra of fluorescence and circular dichrosim. Stopped-flow studies show that there are at least two steps during the interaction of Zn(II) with the apo form. In comparison with its apo form, the native beta-NGF shows a higher ability to trigger the proliferation of TF1 cells and mediate the survival of PC12. Thus it is most likely that the structural changes caused by the presence of Zn(II) directly lead to the increase in the biological activity of beta-NGF. All results indicate that Zn(II) in native beta-NGF plays an important role in the structure and the biological activity of the protein.