Figure 5

Detailed structural analysis of different residues in the DNA binding domain of AmtR. Panels (A) and (B): Location and interactions of the non-interface residues that were experimentally investigated. Surface-exposed residues are depicted as sticks, while those residues that are buried in the interior of the protein are shown in space-filled presentation. Panels (C) to (F): Interactions of the residues located in the protein DNA interface. The DNA backbone is shown as grey tube and nucleotides of the binding site are shown in stick presentation. Contacts are indicated by dotted lines. The residues shown in (F) might play a dual role by forming both contacts with the DNA and with other parts of the protein. A water molecule, which was modeled in analogy to the TetR-operator complex crystal structure, is shown as green ball. See text for more details.