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 *******************************************