Pneumococcus is among the world’s leading bacterial pathogens and is responsible for over 1 million deaths annually. Transition metal ions, such as Zn(II), have been recognized as essential nutrients for the growth and virulence of pathogenic bacteria, including pneumococcus, in humans. Acquisition of Zn(II) in pneumococcus is supported by the ATP-binding cassette transporter AdcBCA, which includes surface proteins AdcA and AdcAII as the initial receptors for Zn(II) recognition. AdcAII is a high affinity Zn(II)-specific solute-binding protein and it plays an imperative role in the survival and pathogenicity of pneumococcus. To date, the crystal structure of AdcAII in the closed conformation has been determined. However, structural information of AdcAII in the open state was still not available, which hindered deeper understanding of the Zn(II) acquisition mechanism in pneumococcus. In this study, we determined the crystal structures of AdcAII in its partially open conformations by X-ray crystallography. Comparing the crystal structures of AdcAII both in its closed and open conformations reveals significant conformational changes in two loops above the Zn(II)-binding site. In the Zn(II)-bound closed conformation, the loops fold onto the binding site and trap the bound Zn(II) within. In comparison, in the open conformation, the two loops move away from the binding site and expose the binding cavity to the bulk solvent. These new structural insights allows us to construct the first molecular model that forwarded our understanding in Zn(II) acquisition mechanism by AdcAII in pneumococcus.