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. Author manuscript; available in PMC: 2009 Oct 1.
Published in final edited form as: Curr Opin Struct Biol. 2009 Apr 10;19(2):171–177. doi: 10.1016/j.sbi.2009.03.002

Figure 3. Recognition of minor grove shape and electrostatic potential by a Hox homeodomain.

Figure 3

- Crystal structures of Scr bound to its specific fkh250 sequence, PDB code 2r5z (A), and the Hox consensus sequence fkh250con*, PDB code 2r5y (B). Color coding of the molecular surface reveals, for the fkh250 site, an extended region with a narrow minor groove, which binds His-12, Arg3, and Arg5. In contrast, the minor groove of the fkh250con* site is only narrow at the local region that binds Arg5. A mesh of the -8kT/e isosurface illustrates that the electrostatic potential, as calculated with DelPhi [35], is more negative in the minor groove of the fkh250 site than in the fkh250con* site. MC simulations of the free binding sites indicate the distinct minor groove shape to be an intrinsic feature of the free binding sites (see text). Molecular shape and electrostatic isosurface representations were generated with GRASP2 [56].