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. Author manuscript; available in PMC: 2011 Aug 10.
Published in final edited form as: Biochemistry. 2010 Aug 10;49(31):6784–6790. doi: 10.1021/bi100839e

Figure 2.

Figure 2

A slight shift in position of the nucleoside, plus adjustment of the side chains of Glu53 and Arg104, allow WT dCK to accommodate the additional methyl group present in 5-Me-dC versus dC. (A) Superposition of the WT dCK D-dC+ADP complex (green; PDB ID 1P5Z) on the WT dCK 5-Me-dC+ADP complex (gray). 5-Me-dC is positioned slightly further from Arg104. (B) A theoretical model of 5-Me-dC (yellow) were it to bind at the same position as D-dC. Such a binding mode would produce unfavorable close contacts with Glu53 (2.6 Å) and Arg104 (2.8 Å). (C) The adjustments made by the active site residues due to the methyl group of 5-Me-dC include a shift of the side chain of Glu53 by 0.6 Å, Arg104 by 0.5 Å, and the nucleoside itself by 0.2 Å. The shift of Glu53 increases the distance to the methyl group from otherwise 2.8 Å to 3.4 Å.