19 bp DNA 1D66-PWZ Protein for Molecular Biology

Whole complex.
Rotate:

Y -90�
Distances:

DNA Double a-helix (19 bp length in � units)

Dimameter of Double a-Helix (length in � units)

Reset
1D66 DNA 19 bp GAL4 The Overall Architecture of DNA .
The yeast GAL4 Protein is a transcriptional activator that binds to DNA. The DNA 19bp is shown using Sticks with the bases colored Shapely, and the backbone colored red. The two 2 subunits of the symmetric dimer are shown using the Backbone display. The DNA recognition module is blue; the linker region is purple; and the dimerization element is green. The two 2 metal ions bound to each subunit are shown as yellow balls. (cf. Fig. 3 of Marmorstein, et al.)

Close-up view of protein-DNA interactions in one half-site.
Protein residues H-bond to the DNA bases as follows: Lys17 (carbonyl) to C8; Lys18 (carbonyl) to C7 and C8; and Lys18 (amino) to G6 and/or G7.
The protein also makes these contacts to the DNA sugar-phosphate backbone: Gln9 and Arg15 with phosphate 5; and Lys20, Cys21 (NH), and Lys23 with phosphate 6. (cf. Figs. 5 & 6 of Marmorstein, et al.)
Show H-bond distances to:

DNA backbone.
(Zoom-in to see the individual contacts.)

Viewing tips:
Use the buttons to the right of the image to show only portions of the structure; then use the Chime menu to display or color the molecule. The rotate buttons act on the entire structure. Remove the distance monitors with a second click.

Go to the one-page display of one of these structures:

Back to Structures for Molecular Biology at CMU.

The image displayed on this page requires the Chemscape Chime plug-in.
A description of its use at this site can be found at the Chime Features page.

Coordinates from 1D66.pdb.