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. 2010 Mar 30;2(4):900–926. doi: 10.3390/v2040900

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© 2010 by the authors; licensee Molecular Diversity Preservation International, Basel, Switzerland.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).

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Figure 3. — The chemistry of RNase H cleavage is believed to be a two-metal ion mechanism. A Two divalent metal ions (red spheres, marked A and B) are coordinated by the active site residues D549, D443, D498 and E478 approximately 4Å apart. Metal ion A activates a water molecule. B The activated water molecule carries out a nucleophilic attack (blue arrow) driving the phosphoryl transfer reaction. C In the putative transition state, the metal ions move toward each other to bring the nucleophile within range of the scissile phosphate. D The reaction products consist of a 3′ OH group and a 5′ phosphate group, and the metal ions are again likely to be re-positioned.