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Metal-substituted crystals of human carbonic anhydrase II belonging to space group P21 with cell dimensions a = 42.7, b = 41.7, c = 73.0 Å and β = 104.6° were analyzed crystallographically. The resolution limit ranged from 1.82 to 1.92 Å with high completeness (86.2–90.7%). Cobalt(II)-substituted carbonic anhydrase has a tetrahedral coordination around the metal both at pH 6 and pH 7.8, similar to the native zinc enzyme. In contrast, the catalytically inactive copper(II), nickel(II) and manganese(II) derivatives showed increased coordination number around the metal ion. Whereas the copper is best described as penta-coordinated, the nickel and manganese are best described as hexa-coordinated. The results are briefly compared with spectroscopic observations and our current view on carbonic anhydrase catalysis.