Figure 3.
Fig. 3. The metal center. A, the 2F[o] F[c]
electron density map in the zinc center contoured at the 3 level and
is shown in green, and the weak density in the 2F[o] F[c] map
for the loosely bound zinc ion contoured at the 2 level and
is shown in purple. The structural refinement revealed that the
enzyme binds two zinc ions with very different affinities. B,
superposition of the bi-nickel center in urease (Protein Data
Bank code 1UBP), the mononuclear iron center in cytosine
deaminase (Protein Data Bank code 1K6W), and the bi-zinc center
in D-aminoacylase, shown in red, blue, and green, respectively.
The
metal-binding site is more buried, while the site is
more solvent-exposed. The residue numbering is labeled in the
same color for each protein. The critical hallmark for the
binuclear subset is a carboxylated lysine residue serving as a
bridging ligand. A cysteine residue (Cys96) in D-aminoacylse,
and the third conserved histidine (His214) in cytosine
deaminase, compensate the missing carboxylated lysine.
F[c]
electron density map in the zinc center contoured at the 3 
level and
is shown in green, and the weak density in the 2F[o] 
metal-binding site is more buried, while the 
site is
more solvent-exposed. The residue numbering is labeled in the
same color for each protein. The critical hallmark for the
binuclear subset is a carboxylated lysine residue serving as a
bridging ligand. A cysteine residue (Cys96) in D-aminoacylse,
and the third conserved histidine (His214) in cytosine
deaminase, compensate the missing carboxylated lysine.