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. 2012 Sep 25;287(48):40099–40105. doi: 10.1074/jbc.M112.413054

FIGURE 3.

FIGURE 3.

DNA sequence-specific contacts in InC and ExC. A and C, stereoview of the protein-DNA interface in InC (A) and ExC (C), focusing on sequence-specific contacts between the major groove surface of the recognition site in DNA and amino acid side chains of M.HaeIII. The base pairs are individually color-coded as in Fig. 1, although the 5′-to-3′ orientation of the duplex is opposite in Figs. 1 and 3. Amino acid side chains of residues that make sequence-specific hydrogen bonding interactions are shown, with dashed lines denoting hydrogen bonds. B and D, schematic representation of contacts in the protein-DNA interface of InC (B) and ExC (D). The residues named in black, blue, and red make the indicated hydrogen bonds solely via their side chain, main chain, or both kinds of atoms. Only those interfacial water molecules that are present in Mols A–C and that are made via a solitary water molecule are shown. The intercalating side chain of Ile-221 is shown in gray in all four panels.