Suggested way to use this chime page.

Mouse action summary

Fist explore the enzyme-DNA complex in the original ribbon and backbone mode. (Just click the "Select whole complex and resize" button or hit reload on your browser to get to the original presentation.)

The form of the enzyme that was crystallized has two domains, a 3' to 5' exonuclease domain and the polymerization domain. Use the buttons to highlight each.

Now look at the substrates: DNA, the incoming nuleotide, and 2 magnesium ions. Identify the template and primer strands. When you restrict to just the substrates, there is an extra base hanging away from the double-helical portion of the DNA. What is it? (Try to answer, then click here.)

How far is the polymerization active site from the exonuclease domain? You can get distances as follows: From the menu choose "Select >> Mouse Click Action >> Distance." Now distances are given between successive mouse clicks. Answer
Obviously, a major rearrangement of the path of the primer strand through the enzyme is required for editing.

Let's investigate the active site. Notice how the incoming nucleotide has positioned itself so that it is in the right position to bocome B-DNA. Reset the image and then click Retrict under "Substrates: DNA and dNTP", zoom in a bit. Once you are oriented show all of the atoms. If you lose the incoming dNTP, color its carbons white. Observe how the 3'-OH of the primer is situated so that it can attack the phosphorous of the alpha-phosphate of the incoming dNTP.

Now, reset the image and click "Highlight active site." Then click "Zoom in on the active site." Get oriented. Color the primer and the template; reset the colors by clicing the zoom buttons again. Once again look at the positioning on the 3'-OH and the alpha phospahte.  The reaction that creates the new phosphoester bond is an SN1 displcement on the phosphorous of the alpha phosphate. The 3'-OH is the nucleophile and the beta phosphate is the leaving group. To make the 3'-OH a better nucleophile, it must lose its hydrogen. Is there a suitable group around to accept this hydrogen? I'm not certain , but my gueuss is . Similarly, to make the beta phosphate a better leaving group, it should be protonated. Which residue might donate such a proton? My choice is .

Remember, if the image gets too messed up, just click the select whole complex button or reload.