As part of an effort to inhibit S100B, structures of pentamidine (Pnt) bound to Ca 2+ -loaded and Zn 2+ ,Ca 2+ -loaded S100B were determined by X-ray crystallography at 2.15 Å (R free = 0.266) and 1.85 Å (R free = 0.243) resolution, respectively. These data were compared to X-ray structures solved in the absence of Pnt, including Ca 2+ -loaded S100B and Zn 2+ ,Ca 2+ -loaded S100B determined here (1.88 Å; R free = 0.267). In the presence and absence of Zn 2+ , electron density corresponding to two Pnt molecules per S100B subunit was mapped for both drug-bound structures. One Pnt binding site (site 1) was adjacent to a p53 peptide binding site on S100B (±Zn 2+ ), and the second Pnt molecule was mapped to the dimer interface (site 2; ±Zn 2+ ) and in a pocket near residues that define the Zn 2+ binding site on S100B. In addition, a conformational change in S100B was observed upon the addition of Zn 2+ to Ca 2+ -S100B, which changed the conformation and orientation of Pnt bound to sites 1 and 2 of Pnt-Zn 2+ ,Ca 2+ -S100B when compared to Pnt-Ca 2+ -S100B. That Pnt can adapt to this Zn 2+ -dependent conformational change was unexpected and provides a new mode for S100B inhibition by this drug. These data will be useful for developing novel inhibitors of both Ca 2+ -and Ca 2+ ,Zn 2+ -bound S100B.