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I agree with Dale that your four metals are not in the density and also don't seem to make sense in terms of chemistry. Based on your residue placement and electron density, it looks more like a non-heme manganese catalase structure where two metal ions bind with very similar environment. This reference may help you. Archives of Biochemistry and Biophysics Volume 525, Issue 2, 15 September 2012, Pages 111–120 Anthony ----------------------------------------------------- Dr. Anthony Addlagatta Center for Chemical Biology Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 Web: https://sites.google.com/site/chembioliict/home/dr-anthony-addlagatta-1 ---------- Original Message ----------- From: Dale Tronrud <det...@uoxray.uoregon.edu> To: CCP4BB@JISCMAIL.AC.UK Sent: Wed, 16 Jan 2013 14:14:50 -0800 Subject: Re: [ccp4bb] how many metal sites > *********************** > This message has been scanned by the InterScan for CSC SSM at IICT and found > to be free of known security risks. > *********************** > > Zn is a very electron rich atom so a 2.3 A resolution data set should > be a fine experiment to determine the number of fully occupied metal > sites. It is always hard to be sure about screen shots of density, but > it looks to me that you only have evidence for one zinc here. > > In my opinion, it is not useful to build models that don't make > sense. Your zinc cluster does not make chemical sense to me and > the atoms are not in the density. I suspect that you built this > cluster, and not the obvious model with fewer zinc atoms, simply > because you wanted to match the "magic number" of four. Use the > things you know with confidence as your guide. > > Dale Tronrud > > On 01/16/13 11:15, ruisher hu wrote: > > Hi, Dear All, > > > > I recently got a dataset about 2.3 A resolution, however, I got some > > trouble assigning the metal sites. It suppose to have multiple binding > > site(possibly four) around those four glu residues in the center (see > > the attached figure), however, it shows up a huge single positive > > density ,clustered in the binding center. The signal is pretty strong > > and I think zn is definitely there. When I tried to put four zns around, > > the geometry doesn't look very good and there is still some positive > > density in the center (although get weaker) and the bfactor of metals > > are high like 100. Does anyone know what's going on?Does it mean only > > one single site in the middle?Or maybe just metals are too mobile? > > What's the best way to tell how many metal sites are actually > > there?Which experiment can I use to test? Thanks very much. > > > > Best, > > > > R > > > > On Wed, Nov 7, 2012 at 9:29 AM, SD Y <ccp4...@hotmail.com > > <mailto:ccp4...@hotmail.com>> wrote: > > > > Dear all, > > > > I have a related question to the one I have posted "low resolution > > and SG", on which I am still working based on the suggestions I have > > got. > > > > The model I have used, has Zn co-ordinated well in tetrahydral > > fashion by 3 cys and 1 His residues. They have add Zn in to their > > experiment. > > In my 3.4 A structure (I am still working on right SG), initial > > maps show very strong positive density (sigma=6.5) at the place of > > Zn > > ( https://www.dropbox.com/s/4jd6gdor87ab9lj/Zn-coordination.png). I > > have not used Zn in my experiment. I could only suspect Tryptone and > > yeast extract which I used to make media. > > > > I would like to know how likely this positive density belongs to > > Zn? How to reason the presence of Zn when its not been used? > > Is there is any way to confirm if its Zn. If this is not Zn, what > > else could it be? Any thing I could try to rule out or in Zn or > > other ions. > > I appreciate your help and suggestions. > > > > Sincerely, > > SDY > > > > ------- End of Original Message ------- This Mail Scanned by ClamAV and Spammassassin
