Re: [ccp4bb]: Mg coordination and h-bonding

[Susan Heffron <sheffron@uci.edu>]

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Thanks very much for the replies, especially Tom Hurley and Greg Verdon. I'll do
the analysis of donors and acceptors, considering hydrogens and lone pairs and
geometry.  From a preliminary look, I think there are some hydrogen bonds,
though of course not as many as it might seem just by looking at a list of
distances.  Just to clarify, although it is difficult to depict the
3-dimensional arrangement in simple 2D, my drawing should have been more like:

         (front)  (back)
         Lig1_1   Lig1_2
              \  /
    Thr_OG1 -- Mg -- Wat1
              /  \
           Wat2   Lig2
         (front) (back)
   
Sorry for the confusion.  Thanks again to all who responded.

                           Susan

"Hurley, Thomas D." wrote:
> 
> Susan,
> 
> Maybe I'm confused by the arrangement you drew, but I don't see how the Threonine could hydrogen bond to a ligand atom that is in an axial position respect to the threonine.  It could be possible providing the ligand atom is in the equatorial plane of the metal geometry, but not if it was in the opposite axial position.  Additionally, one lone pair of the hydroxyl oxygen is utilized by coordination to the metal, so the other possible interactions would have to be the donation of a hydrogen by the threonine to one ligand atom and the acceptance of a hydrogen from the other ligand atom to the second lone pair of the hydroxyl oxygen.  Do the ligands have the possibility to participate in this way, eg. are there lone pairs or hydrogens available from those ligand atoms?
> 
> Tom Hurley
> Indiana University
> 
> -----Original Message-----
> From: Susan Heffron [mailto:sheffron@uci.edu]
> Sent: Thursday, February 13, 2003 9:20 PM
> To: ccp4bb@dl.ac.uk
> Subject: [ccp4bb]: Mg coordination and h-bonding
> 
> ***  For details on how to be removed from this list visit the  ***
> ***          CCP4 home page http://www.ccp4.ac.uk         ***
> 
> Hi!
> 
> When protein and ligand atoms are coordinating to a Mg2+ ion, can these same
> atoms be considered to interact with each other to form hydrogen bonds?
> 
> I am trying to list the h-bonds from ligands to protein in my structure, and I
> have the following sort of arrangement:
> 
>         Wat1   Wat2
>            \  /
>   Thr_OG1 - Mg - lig1_atom1
>            / \
>         lig2  lig1_atom2
> 
> For instance, this Thr is within h-bonding distance of lig1_atom1 and
> lig1_atom2, but I don't know whether to consider these real hydrogen bonds, or
> whether they would be "blocked" by the interaction with the Mg2+.  What do you
> think?
> 
> Thanks in advance.
> 
>                          Susan
> 
> --
> ------------------------------------------------------------------
>         Susan Heffron
> Dept. of Physiology and Biophysics
> University of California, Irvine
>  Irvine, CA  92697-4560   U.S.A.
>     phone:  (949) 824-4625
>     FAX:    (949) 824-8540
> ------------------------------------------------------------------

-- 
------------------------------------------------------------------
        Susan Heffron
Dept. of Physiology and Biophysics                               
University of California, Irvine                
 Irvine, CA  92697-4560   U.S.A.                         
    phone:  (949) 824-4625
    FAX:    (949) 824-8540
------------------------------------------------------------------