Marine mussels tether to seashore surfaces with byssal threads, proteinaceous fibers that effectively dissipate energy from crashing waves. Protein metal coordination bonds have been proposed to contribute to the characteristic mechanical and self-healing properties of byssal threads; however, very little is understood about how these cross-links function at the molecular level. In the present study, combined Raman and X-ray absorption spectroscopy (XAS) measurements were employed to confirm the presence of protein-Zn2+ coordination bonds in the mussel byssus and to monitor transitions in the coordination structure during thread deformation and self-healing. Results indicate that Zn2+ coordination bonds, primarily mediated via histidine, are ruptured during thread yield and reformed immediately following thread relaxation. Mechanical healing, on the other hand, is correlated with the transition toward shorter coordination bond lengths. Calculation of the healing activation energy suggests that protein-Zn bond exchange provides a primary rate-limiting step during healing.