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Is it possible that the phosphates are just disordered rather than being cleaved? It's always the case for inactive kinase-ATP or AMPPNP complexes that the phosphates are not stabilized by Mg2+ or the residues in the binding pocket and hence they become disordered and are not seen in the electron density. It may be worth to take a look at those phosphate-binding residues in your enzyme and see if they are positioned towards your AMPPNP's phosphates. HTH, Matt On Mon, Feb 14, 2011 at 5:30 AM, Soisson, Stephen M < [log in to unmask]> wrote: > Hi there, > > Was recently looking at a structure of an enzyme with AMP-PNP added to the > crystallization mix, and all I see is density for ADP. I was wondering if > hydrolysis of AMP-PNP to ADP is relatively common - either as a result of > extended time in crystallization or exposure of the resultant crystals to > synchrotron radiation? > > I know that there can be up to 10% contamination of ADP in the purchased > material, so it could just be that we have selected that form in the > crystal, or that there was endogenous ADP bound that failed to substitute. > Just curious if hydrolysis is a common observation. > > Thanks in advance- > > Steve > > Stephen M. Soisson, Ph.D. > *Structural Chemistry Site Lead, WP* > > Merck Research Laboratories > 770 Sumneytown Pike, WP14-1101 > West Point, PA 19486 > Phone: (215) 652-6185 > Fax: (215) 652-9051 > [log in to unmask] > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > > -- -------------------------------------------------------------------------------------------- Matthew L.H. Chu, PhD Postdoctoral Scholar - Weis Lab Department of Structural Biology Fairchild D143, MC 5126 Stanford School of Medicine Stanford, CA 94305-5432 --------------------------------------------------------------------------------------------