The starting display shows the DNA as sticks with white backbone and green bases. The 5' and 3' ends are labeled. The subunits of the EcoRI homodimer are labeled at their C-termini. Note the kink in the DNA at the center of the structure. This localized, four base pair distortion widens the major groove, making it fully accessible to the Eco RI recognition regions.
The Scale of Things: How long is the bound DNA (12 base pairs)? To find out do the following:
Select¬Mouse Click Action¬Toggle Distance Monitor
Now use the right mouse button to click on two atoms at the ends of the DNA to find the distance between them. After you are done you probably want to reload the page by clicking in the left frame.
Selection of DNA: The two protein monomers are associated with chains A and C. The two strands of the DNA are associated with chains B and D. To change the rendering of DNA to Ball & Stick do the following:
Select¬Chain¬B
Select¬Modify Selection Mode¬Add to Selection
Select¬Chain¬D
Display¬Ball & Stick
Note that the 2nd command, "Modify Selection Mode ¬ Add to Selection", added the second selection (chain D) to the first, such that the last command acted on both DNA chains. Before continuing you probably want to undo this:
Select¬Modify Selection Mode¬Replace Selection
Highlight the AATT Sequence:
Select¬Nucleic¬AT
Select¬Change Color To¬Yellow