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Conclusion

The DNA binding sites are shown here in red and the active site is shown in blue. By rotating the model around, you can see how the DNA would fit into the enzyme, positioning it for attack by the active site.

Here is the same view except the areas of interest are spacefilled.

Here is a view showing you the residues that bind to the major groove of the DNA. (orange) And the residues that bind to the minor goove of the DNA. (pink) You can see how the DNA would be nestled in the center of the cavity.

Here is a view that is showing you the above and the active His309. (purple)

It is interesting to note that at the Wells center for Pediatric Research, researches there have developed a fully functional chimeric protein that contains both 06-methylguanine DNA methyltransferase and HAP1. Both proteins retained their function and it is promising to think that it might be used for some type of therapy for certain cancers.