Re: [ccp4bb] Mg++ binding to N7 of G
Hi Bill, On Apr 2, 2008, at 10:58 PM, William G. Scott wrote: I've got what appears to be an inner-sphere interaction between Mg++ and the N7 of a G. The mode of binding is the same as what is observed at this site for Mn++, confirmed with anomalous data. Our resolution is 1.6 Å, so I am reasonably confident this is right. However, my chemist's viewpoint is that Mg++ is too hard and N is too soft for this to happen. I would also be hesitant. Since Mg++ has the same number of electrons as water and no useful absorbance, it seems assigning them based on hydration geometry and bond distances is the only hope. One can often see magnesium ions in anomalous-difference fouriers with good home-source data. Since you appear to have very good diffraction and your magnesium is most definitely relatively well ordered (if it is a magnesium..) I think it is worth a try to carefully collect a data set using a wavelength around 1.5-1.6 Å (or simply your home source depending on how good it is). Cheers, Martin . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Nobels väg 3 SE-171 77 Stockholm Sweden
Re: [ccp4bb] Mg++ binding to N7 of G
William, it is not clear from your message why you think this is a Mg++, not Mn++ which has been observed in this site before? Mn++ would be visible in anomalous data from a home source, but not Mg++. The only way to distinguish Mg++ and water is the number of coordination which should be very clearly organized around a Mg++. You could propably also tell by the bond lengts as the Mg-O coordination should be 2.1-2.2, water hydrohgen bonding around 2.7 Å Could the atom be Zn++ or Na+ ? Pirkko Heikinheimo Martin Hallberg wrote: Hi Bill, On Apr 2, 2008, at 10:58 PM, William G. Scott wrote: I've got what appears to be an inner-sphere interaction between Mg++ and the N7 of a G. The mode of binding is the same as what is observed at this site for Mn++, confirmed with anomalous data. Our resolution is 1.6 Å, so I am reasonably confident this is right. However, my chemist's viewpoint is that Mg++ is too hard and N is too soft for this to happen. I would also be hesitant. Since Mg++ has the same number of electrons as water and no useful absorbance, it seems assigning them based on hydration geometry and bond distances is the only hope. One can often see magnesium ions in anomalous-difference fouriers with good home-source data. Since you appear to have very good diffraction and your magnesium is most definitely relatively well ordered (if it is a magnesium..) I think it is worth a try to carefully collect a data set using a wavelength around 1.5-1.6 Å (or simply your home source depending on how good it is). Cheers, Martin . B. Martin Hallberg, PhD Assistant professor Department of Cell and Molecular Biology Medical Nobel Institute Karolinska Institutet Nobels väg 3 SE-171 77 Stockholm Sweden -- Pirkko Heikinheimo Structural Biology and Biophysics, Institute of Biotechnology, P. O. Box 65, FIN-00014 University of Helsinki, Finland Visit address: Biocenter 3, room 4320 Viikinkaari 3, 00790 Helsinki, Finland http://www.biocenter.helsinki.fi/bi/xray/pirkko e-mail: [EMAIL PROTECTED] phone: 358-(0)9-191 58957 gsm:358-(0)50-354 0713 fax:358-(0)9-191 59940
[ccp4bb] Mg++ binding to N7 of G
Howdie folks: I've got what appears to be an inner-sphere interaction between Mg++ and the N7 of a G. The mode of binding is the same as what is observed at this site for Mn++, confirmed with anomalous data. Our resolution is 1.6 Å, so I am reasonably confident this is right. However, my chemist's viewpoint is that Mg++ is too hard and N is too soft for this to happen. I looked in a database called http://merna.lbl.gov for Mg++ binding sites, and a bunch pop up for inner-sphere N7 interactions with Mg++. However, if I restrict the search to structures having 1.8 Å resolution or better, the number goes to zero. Since Mg++ has the same number of electrons as water and no useful absorbance, it seems assigning them based on hydration geometry and bond distances is the only hope. Does anyone have anything more definitive I can refer to? Thanks. Bill Scott
Re: [ccp4bb] Mg++ binding to N7 of G
Sorry, I should have been less cryptic: On Apr 2, 2008, at 2:13 PM, Jacob Keller wrote: Forgive the naive questions: To what do the terms hard and soft refer here? In inorganic chemistry, hard refers to bonding where the Coulomb potential dominates, and soft where orbital terms dominate. If one partner prefers electrostatic interactions and the other more covalent- like interactions, the interaction is less probable. So Mg++ likes oxygen, Mn++ likes Nitrogen. And G, I assume, is glycine, Guanine but what is N7? Purine numbering... JPK *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: William G. Scott [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Wednesday, April 02, 2008 3:58 PM Subject: [ccp4bb] Mg++ binding to N7 of G Howdie folks: I've got what appears to be an inner-sphere interaction between Mg++ and the N7 of a G. The mode of binding is the same as what is observed at this site for Mn++, confirmed with anomalous data. Our resolution is 1.6 Å, so I am reasonably confident this is right. However, my chemist's viewpoint is that Mg++ is too hard and N is too soft for this to happen. I looked in a database called http://merna.lbl.gov for Mg++ binding sites, and a bunch pop up for inner-sphere N7 interactions with Mg++. However, if I restrict the search to structures having 1.8 Å resolution or better, the number goes to zero. Since Mg++ has the same number of electrons as water and no useful absorbance, it seems assigning them based on hydration geometry and bond distances is the only hope. Does anyone have anything more definitive I can refer to? Thanks. Bill Scott
