Hi Michael:
It always makes me happy to see that there are people who care about this.
3.3 to 3.4 Å should be an ideal distance for this, and, as you note, the lone pair
residing on the (sp^3-hybridized) nitrogen would have to be oriented for
favorable overlap, which is a bit harder to deduce from your figure.
The other rotomer would place oxygen at that position. Because it is double-bonded
to the gamma carbon, the lone pairs are oriented differently, and the pi-bond would
be approximately parallel to the plane containing the tryptophan, which would give
a nice pi-stacking interaction similar to what is seen with adjacent base pairs in nucleic acids.
Expectation bias, as well as having partial charges turned on during refinement, might
influence the rotomeric state of examples from the PDB, so be careful of social consensus.
With classical electostatics, N has a partial positive charge, and O has a partial negative
charge. (If you think about it, all pi-stacking interactions, from the point of view of classical
electrostatics, would be somewhat repulsive.)
Good luck with this, and let us know of the outcome.
Bill
William G. Scott
Director, Program in Biochemistry and Molecular Biology
Professor, Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
University of California at Santa Cruz
Santa Cruz, California 95064
USA
http://scottlab.ucsc.edu
> On Nov 10, 2018, at 1:45 AM, Michael Jarva <[log in to unmask]> wrote:
>
> Dear ccp4 community,
>
> I have recently been working with a structure that has an Asparagine that makes a planar stacking connection with a Tryptophan ring (pep_ASN-TRP_v2.png), that seem to be a true pi-stacking interaction and I'd like to find more examples of this.
>
> I've found a few other examples in the literature but they are mostly amide hydrogen-pi interactions (4PTI_ASN-TYR_v2.png and 1N4W_ASN-FAD_v2.png), which can be seen by the way the Asn is dipping down into the pi-cloud. One potential exception is of a DNA-binding protein where the orientation is more planar (3HXQ_GLN-DNA_v2.png).
>
> So, I'm looking for examples of Asparagine or Glutamine pi-stacking and am sure there are more of them out there and would greatly appreciate any examples.
>
> best regards
> Michael
>
> Michael Jarva, PhD
> ACRF Chemical Biology Division
> The Walter and Eliza Hall Institute of Medical Research
> 1G Royal Parade
> Parkville Victoria 3052
> Australia
> Phone: +61 3 9345 2493
> Email: [log in to unmask] | Web: http://www.wehi.edu.au/
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> Australian Cancer Research Foundation
>
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> <pep_ASN-TRP_v2.png><4PTI_ASN-TYR_v2.png><3HXQ_GLN-DNA_v2.png><1N4W_ASN-FAD_v2.png>
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