FIGURE 5.
Interactions between Ms6564 and its operator. A, schematic representation of Ms6564-DNA contacts. Rectangles, bases; P, phosphate; sugar ring, deoxyribose; gray circles, water molecules. The sugar ring is numbered. Hydrogen bonds between amino acids and base pairs are represented by red arrows. Hydrogen bonding interactions between amino acids and the DNA backbone are represented by green arrows. The dotted arrows represent hydrogen bonds mediated by water molecules. The base pairs in gray indicate the DNA sequence motif. B, close-up views of direct base pair recognition in the major groove. After DNA binding, the positively charged Lys-47 and negatively charged Glu-37 residues interact with each other (left panel). The hydrogen bonds (dotted lines) between Lys-47 and guanine and between Gln-48 and cytosine, are shown in the middle. Although Lys-47 exhibits specific recognition of guanine, Gln-48 can also make hydrogen bonds with adenine (right panel). The dashed lines represent hydrogen bonds, and only one DNA strand is shown for simplicity. Electron density maps (2Fo − Fc) are contoured at the 1.5 σ level (blue mesh).