what is the .odp file extension?

JPK

On Mon, Dec 20, 2010 at 3:48 PM, Robbie Joosten
<robbie_joos...@hotmail.com> wrote:
> Dear jlliu liu,
>
> Also note that Mg2+ is significantly smaller than water. It fits in places
> where water cannot go. This doesn't look like a magnesium site on first
> glance. If you can (privately) give the PDBid of the previous publication, I
> can have a look in 3D.
>
> Cheers,
> Robbie
>
>> Date: Mon, 20 Dec 2010 21:31:58 +0000
>> From: p...@mrc-lmb.cam.ac.uk
>> Subject: Re: [ccp4bb] Mg2+ or water
>> To: CCP4BB@JISCMAIL.AC.UK
>>
>> Mg2+ is (almost) aways octahedrally coordinated, usually by oxygen atoms,
>> with distances of ~2A.
>> Phil
>>
>> On 20 Dec 2010, at 21:16, jlliu liu wrote:
>>
>> > Hi All,
>> >
>> > I am refining a structure and encountered a problem of modeling a
>> > difference density as water or Mg2+, and would like to hear opinions from
>> > the community. It has the following coordinations (attached): the 
>> > water/Mg2+
>> > forms salt bridge/H-bonding interaction with a carboxylate group from the
>> > ligand, it also forms salt bridge/H-bonding interaction with a Glu residue
>> > from the protein, it is also within hydrogen bonding distance to the main
>> > chain N of another protein residue. In provious publication, it was 
>> > modelled
>> > as a Mg2+ and the author reasoned the dual salt-bridge stabilizes the
>> > liganding binding, also the Mg2+ is present in the protein solution for
>> > crystallization. For my case, I have no Mg2+ present in the protein buffer,
>> > also modelling it with water refines perfectly with no indication of
>> > positive difference density even at 2.0 sigma cut off. Should I modelled
>> > this density as water or as Mg2+. Your opinions are appreciated.
>> >
>> > JL
>> >
>> >
>> > <test.png.odp>
>



-- 
*******************************************
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
cel: 773.608.9185
email: j-kell...@northwestern.edu
*******************************************

Reply via email to