The interaction between biomolecules and inorganic materials has gained much interest for the development of sensors and highly controlled materials in scale and composition. For this purpose, 4F2, a VHH antibody with high affinity and specificity toward zinc oxide (ZnO) surfaces has been constructed. Here, we report that 4F2 also has an affinity toward zinc ion (Zn2+). The stability of 4F2 and its Zn2+ complexes was determined using differential scanning calorimetry. We then determined the binding affinity between 4F2 and Zn2+ by using isothermal calorimetry. To further elucidate the molecular binding mechanism of 4F2 toward Zn2+, we applied the 1H15N heteronuclear single quantum coherence NMR technique. We found that 4F2 recognized Zn2+ near the complementarity determining region 3 (CDR3). Our results provide the basis for the recognition mechanism of ZnO by 4F2.