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. Author manuscript; available in PMC: 2011 Mar 26.

Published in final edited form as: J Mol Biol. 2010 Jan 22;397(2):600–615. doi: 10.1016/j.jmb.2010.01.033

Fig. 2 — Comparing 1WKN.pdb (a), and most other published models of integrase that contain two magnesium ions in the active site, to our new models of integrase (b). Before we developed the Mg-O restraints, the coordination spheres of the magnesium ions displayed less-favorable geometries and improper bidentate interactions with the two Mg’s, similar to the flaws in the published model 1WKN.pdb⁸,⁹. Coordinations are displayed as dashed lines between a carboxylate group and a green sphere that represents a magnesium ion (at reduced size to enhance clarity). Note: the newest model from the Chimirri group contains only one unfavorable bidentate coordination.¹⁵

Fig. 2 — Comparing 1WKN.pdb (a), and most other published models of integrase that contain two magnesium ions in the active site, to our new models of integrase (b). Before we developed the Mg-O restraints, the coordination spheres of the magnesium ions displayed less-favorable geometries and improper bidentate interactions with the two Mg’s, similar to the flaws in the published model 1WKN.pdb⁸,⁹. Coordinations are displayed as dashed lines between a carboxylate group and a green sphere that represents a magnesium ion (at reduced size to enhance clarity). Note: the newest model from the Chimirri group contains only one unfavorable bidentate coordination.¹⁵