Re: [ccp4bb] Mystery density

[Roger Rowlett]

I think a metal ion is unlikely given that the nearest ligand(s) are Arg residues. I would lay money on an anion. The central feature looks very much like a bicarbonate ion, and is very similar to the bicarbonate ion bound in a generic anion binding site near 2 Arg residues on a NCS 2-fold axis in beta-carbonic anhydrase. The rest might be waters. If this sits on a crystallographic symmetry axis, things can look a little funky, but you do seem to have a triangular planar feature in a special position. For a similar binding interaction with bicarbonate, see PDB 3E3I, 3E3F, and Rowlett, et al. (2010) Biochemistry 49, 3640-3647, "Evidence for a Bicarbonate 'Escort' Site in H. influenzae beta-Carbonic Anhydrase." Cheers, _______________________________________ Roger S. Rowlett Gordon & Dorothy Kline Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu On 12/1/2011 4:36 AM, Martin Montgomery wrote: Posting on behalf of Katia Baranova (see below).  Any suggestions gratefully received! Hello, we have a puzzling density and hope someone has an idea of what it may be. The pictures of it are here: http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/top.png http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/front.png http://www.mrc-mbu.cam.ac.uk/sites/default/files/images/mystery/side.png The space group is I422, resolution 1.6A The trial contained Tris, DTT, EDTA, sodium, potassium, phosphate, and chloride. The centre of our unknown feature is about 3.8A from the Arg and it is also on the four fold symmetry axis. It is + 28 sigma in the center and  about + 9.5 sigma in each of the "tentacles". Thank you very much! Katia. On 30 Nov 2011, at 17:30, Katia Baranova wrote: Hello, Well, it doesn't work. Can you forward it please? thanks a lot, K -------- Original Message -------- Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK Date: Wed, 30 Nov 2011 17:27:45 +0000 From: JISCMAIL LISTSERV Server (16.0) <lists...@jiscmail.ac.uk> To: Katia Baranova <e...@mrc-mbu.cam.ac.uk> Listserv does not recognise you as a subscriber to the CCP4BB list using the e...@mrc-mbu.cam.ac.uk address so your message is unable to be distributed. You may be subscribed with a different email address and if you know what that is, re-send from there. If you still have problems, go to www.jiscmail.ac.uk/CCP4BB and subscribe to the list from the link Join or Leave CCP4BB or please contact the list owners at ccp4bb-requ...@jiscmail.ac.uk or helpl...@jiscmail.ac.uk