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. Author manuscript; available in PMC: 2014 Nov 20.
Published in final edited form as: J Am Chem Soc. 2013 Nov 11;135(46):17432–17443. doi: 10.1021/ja408197k

Figure 2.

Figure 2

6-methyl-UMP and 6-amino-UMP complexes. The upper panels show omit electron density maps superimposed on the refined model. Lower panels describe the binding-modes of the various ligands in detail. Red and blue numbers give distances in Ångstroms. (A) WT-MtODCase with 6-methyl-UMP. The omit electron density map was phased without the atoms of the pyrimidine ring, D70, K72, and D75’ included and contoured at 3.5 σ. (B) Conformation A of WT-MtODCase with 6-amino-UMP. The omit electron density map was phased without the atoms of D70 and HOH410 as well as those of the conformation A of K72, D75’ and the pyrimidine ring included and was contoured at 5.5 σ (green) and 3.0 σ (gray). Yellow and gray sticks are conformers A (or the part without alternate conformation) and B, respectively. (C) Conformation B of WT-MtODCase with 6-amino-UMP. The omit electron density map was phased without the atoms of the residues of conformer B (and the part without alternate conformations) included, corresponding to panel B. The green and gray meshes are contoured at 5.5 σ and 3.0 σ, respectively. Yellow and gray sticks are conformers B and A, respectively. (D) K72A-MtODCase with 6-amino-UMP. The omit electron density map (3.0 σ) was phased without the atoms of the pyrimidine ring, D70, D75’, HOH463 and HOH477 included. (E) Conformation A of D75N-MtODCase with 6-amino-UMP. The omit electron density map corresponds to D70 and the pyrimidine ring as well as conformations A of K72 and D75N’. The green and gray meshes represent 8.0 σ and 3.0 σ, respectively. Yellow and gray sticks are conformers A (or the residues without alternate conformation) and B, respectively. (F) Conformation B of D75N-MtODCase with 6-amino-UMP. The omit electron density map was calculated without residues in conformer B (and the part without alternate conformations) included. The green and gray meshes are contoured at 8.0 σ and 3.0 σ, respectively. Yellow and gray sticks are conformers B and A, respectively. This panel is drawn in the same way as panel E, except that conformer B is emphasized (in color) instead of conformer A. The chloride anion, Cl303 (purple), is only observed in conformer B.