Re: [ccp4bb] Mg2+ or water
Hi, you might have a look into the papers of MM Harding. There is a series of papers about metal ions in X-ray structures in Acta D. Look at the number of coordination, geometry and distances. Then you can easily decide whether there is a metal ion and which metal ion it might be. And of course the peak height of anomalous signal (e.g Ca2+, K+) is a hint, but one has to be careful in the case there is not full occupancy. HTH Guenter *Subject:* [ccp4bb] Mg2+ or water 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 -- *** Priv.Doz.Dr. Guenter Fritz Fachbereich Biologie Universitaet Konstanz http://www.biologie.uni-konstanz.de/fritz e-mail: guenter.fr...@uni-konstanz.de e-mail: guenter.fr...@uniklinik-freiburg.de http://www.uniklinik-freiburg.de/neuropathologie/live/forschung/ag-g-fritz.html Tel.: +49 761 270 5078 Fax.: +49 761 270 5050
Re: [ccp4bb] Mg2+ or water
On Dec 21, 2010, at 2:08 AM, Vellieux Frederic wrote: Programs that check viruses in incoming emails remove all files that carry double extensions because this is a way to hide the real nature of the file. This doesn't sound correct, at least not for any antivirus package that is worth the money. Only a subset of file extensions will be executed by Windows automatically. No Microsoft program will yet open an .odp file, so it certainly isn't known as an executable to the OS a priori. If your antivirus program, by default, has the behavior you describe, then you might want to zap it and get something else because it most certainly will be touching junk that it shouldn't and missing other legitimate threats. James
Re: [ccp4bb] Mg2+ or water
You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's algorithm. Cheers, Robbie Date: Mon, 20 Dec 2010 22:59:53 + From: paul.ems...@bioch.ox.ac.uk Subject: Re: [ccp4bb] Mg2+ or water To: CCP4BB@JISCMAIL.AC.UK On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul.
Re: [ccp4bb] Mg2+ or water
Hello, as to the WASP server: We found it to be very useful in the past, but the link is no longer functional! Is there any other address for accessing this server? Oliver PD Dr. Oliver H. Weiergräber Institut für Strukturbiologie und Biophysik ISB-3: Strukturbiochemie Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 From: CCP4 bulletin board [ccp...@jiscmail.ac.uk] On Behalf Of Robbie Joosten [robbie_joos...@hotmail.com] Sent: Tuesday, December 21, 2010 9:55 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Mg2+ or water You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's algorithm. Cheers, Robbie Date: Mon, 20 Dec 2010 22:59:53 + From: paul.ems...@bioch.ox.ac.uk Subject: Re: [ccp4bb] Mg2+ or water To: CCP4BB@JISCMAIL.AC.UK On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul. Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Dr. Ulrich Krafft (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt
Re: [ccp4bb] Mg2+ or water
On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an open document presentation. It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp file is an ISO standard--like the country code you dial when you call your favorite Aunt. You can open a .odp file with the free office suit called OpenOffice. Just download it from http://www.openoffice.org/ and start double-clicking to open the file just like you would if you were using some other presentation software. Also, Jlliu Liu set a good example by sending the document in an open format so anyone can open it (even though some may not have heard of an odp file before). By using an open format, Jlliu Liu has catered to convenience rather than catering to ignorance, and has increased the range of people who can provide him with help. James 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 + 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 ***
Re: [ccp4bb] Mg2+ or water
James Stroud wrote: On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an open document presentation. It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp file is an ISO standard--like the country code you dial when you call your favorite Aunt. You can open a .odp file with the free office suit called OpenOffice. Just download it from http://www.openoffice.org/ and start double-clicking to open the file just like you would if you were using some other presentation software. Also, Jlliu Liu set a good example by sending the document in an open format so anyone can open it (even though some may not have heard of an odp file before). *By using an open format, Jlliu Liu has catered to convenience rather than catering to ignorance,* and has increased the range of people who can provide him with help. James But there was a double extension in the name of the file provided initially (.png.odp if I remember well). Programs that check viruses in incoming emails remove all files that carry double extensions because this is a way to hide the real nature of the file. They also remove .exe files and others (like having too many spaces in a file name). Fred.
Re: [ccp4bb] Mg2+ or water
[christmas flame] The 'hiding' only applies to Windows, and that's your own fault then... and your responsibility to look after it. And since attachments are deprecated on this list it further imposes no real problem at all. [/christmas flame] ;- Tim On Tue, Dec 21, 2010 at 11:08:27AM +0100, Vellieux Frederic wrote: James Stroud wrote: On Dec 20, 2010, at 1:53 PM, Jacob Keller wrote: what is the .odp file extension? http://tinyurl.com/mjokqs A .odp file is an open document presentation. It is the open version of a power point presentation. http://en.wikipedia.org/wiki/OpenDocument An .odp file is an ISO standard--like the country code you dial when you call your favorite Aunt. You can open a .odp file with the free office suit called OpenOffice. Just download it from http://www.openoffice.org/ and start double-clicking to open the file just like you would if you were using some other presentation software. Also, Jlliu Liu set a good example by sending the document in an open format so anyone can open it (even though some may not have heard of an odp file before). *By using an open format, Jlliu Liu has catered to convenience rather than catering to ignorance,* and has increased the range of people who can provide him with help. James But there was a double extension in the name of the file provided initially (.png.odp if I remember well). Programs that check viruses in incoming emails remove all files that carry double extensions because this is a way to hide the real nature of the file. They also remove .exe files and others (like having too many spaces in a file name). Fred. -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] Mg2+ or water
Note that the original Nayal Di Cera algorithm uses an older and less preferred version of the bond valence model and its associated parameters than current implementations of BV. The original WASP uses this formula: bond valence = (Rij/R0)^(-N) The most up-to-date BV parameter set (http://www.ccp14.ac.uk/ccp/web-mirrors/i_d_brown/bond_valence_param/bvparm2006.cif ) uses this: bond valence = exp((Ro-Rij)/B) where Rij is the metal-ligand distance, and R0, N and B are parameters specific to the metal-ligand pair. Obviously these parameter sets may give different results depending on which formula you are using. See the IUCr monograph by I.D.Brown: The Chemical Bond in Inorganic Chemistry: The Bond Valence Model, chapter 3 for more info. Cheers -- Ian On Tue, Dec 21, 2010 at 8:55 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's algorithm. Cheers, Robbie Date: Mon, 20 Dec 2010 22:59:53 + From: paul.ems...@bioch.ox.ac.uk Subject: Re: [ccp4bb] Mg2+ or water To: CCP4BB@JISCMAIL.AC.UK On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul.
Re: [ccp4bb] Mg2+ or water
You might also like to look at the paper Is the bond-valence method able to identify metal ions in protein structures, Acta Cryst. D59 (2003) 32-37. In retrospect, the BV method is very good for identifying Mg2+ because it is almost always tightly octahedrally coordinated by oxygen atoms. For other metals and low resolution the calculation can easily be upset by missing water ligands or inaccurate interatomic distances. If anyone is interested I can supply a powerpoint of the lecture on the BV method from my undergraduate solid state chemistry course, but I should warn you that it is in German (like most of our teaching). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 21 Dec 2010, Ian Tickle wrote: Note that the original Nayal Di Cera algorithm uses an older and less preferred version of the bond valence model and its associated parameters than current implementations of BV. The original WASP uses this formula: bond valence = (Rij/R0)^(-N) The most up-to-date BV parameter set (http://www.ccp14.ac.uk/ccp/web-mirrors/i_d_brown/bond_valence_param/bvparm2006.cif ) uses this: bond valence = exp((Ro-Rij)/B) where Rij is the metal-ligand distance, and R0, N and B are parameters specific to the metal-ligand pair. Obviously these parameter sets may give different results depending on which formula you are using. See the IUCr monograph by I.D.Brown: The Chemical Bond in Inorganic Chemistry: The Bond Valence Model, chapter 3 for more info. Cheers -- Ian On Tue, Dec 21, 2010 at 8:55 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's algorithm. Cheers, Robbie Date: Mon, 20 Dec 2010 22:59:53 + From: paul.ems...@bioch.ox.ac.uk Subject: Re: [ccp4bb] Mg2+ or water To: CCP4BB@JISCMAIL.AC.UK On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul.
Re: [ccp4bb] Mg2+ or water
Yes the BV method relies on summing up the 'bond valence' contributions for each ligand co-ordinated to the metal, and comparing the result with the formal charge on the metal ion (e.g. +2 for Mg). This means that even if say one water that is present in the crystal is omitted from the calculation for whatever reason (say you summed the contributions from only 5 instead of 6 waters because you didn't include the symmetry molecule as in the original version of WASP), then you are likely to conclude from the result that it's not Mg even if the distances and the octahedral co-ordination of the 5 waters that you did include are perfect for Mg. Obviously as George says, if the distances are inaccurate then the computed BV contributions to the sum will be wrong and that's not good either! So I completely agree that it's probably wise to take the results of applying this method with a large pinch of salt! Cheers -- Ian On Tue, Dec 21, 2010 at 12:25 PM, George M. Sheldrick gshe...@shelx.uni-ac.gwdg.de wrote: You might also like to look at the paper Is the bond-valence method able to identify metal ions in protein structures, Acta Cryst. D59 (2003) 32-37. In retrospect, the BV method is very good for identifying Mg2+ because it is almost always tightly octahedrally coordinated by oxygen atoms. For other metals and low resolution the calculation can easily be upset by missing water ligands or inaccurate interatomic distances. If anyone is interested I can supply a powerpoint of the lecture on the BV method from my undergraduate solid state chemistry course, but I should warn you that it is in German (like most of our teaching). George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582 On Tue, 21 Dec 2010, Ian Tickle wrote: Note that the original Nayal Di Cera algorithm uses an older and less preferred version of the bond valence model and its associated parameters than current implementations of BV. The original WASP uses this formula: bond valence = (Rij/R0)^(-N) The most up-to-date BV parameter set (http://www.ccp14.ac.uk/ccp/web-mirrors/i_d_brown/bond_valence_param/bvparm2006.cif ) uses this: bond valence = exp((Ro-Rij)/B) where Rij is the metal-ligand distance, and R0, N and B are parameters specific to the metal-ligand pair. Obviously these parameter sets may give different results depending on which formula you are using. See the IUCr monograph by I.D.Brown: The Chemical Bond in Inorganic Chemistry: The Bond Valence Model, chapter 3 for more info. Cheers -- Ian On Tue, Dec 21, 2010 at 8:55 AM, Robbie Joosten robbie_joos...@hotmail.com wrote: You could also try the original WASP here (also for coloured Indo-dutch catholics): http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl or you can use the latest WHAT_CHECK that also has an implementation of Nayal and Di Cera's algorithm. Cheers, Robbie Date: Mon, 20 Dec 2010 22:59:53 + From: paul.ems...@bioch.ox.ac.uk Subject: Re: [ccp4bb] Mg2+ or water To: CCP4BB@JISCMAIL.AC.UK On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul.
Re: [ccp4bb] Mg2+ or water
Using different web servers on your refined structure is good thing to do. But for distinguishing metal ion, specifically Mg, from water was done unambiguously before these programs existed. The simple rule is two fold: 1. distance; 2. coordination. For Mg ion distances are between 2 and 2.2 A and coordination is almost always nearly perfect octahedron. Neither of those criteria met in your structure. Hence the verdict - it is water. Vaheh From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of jlliu liu Sent: Monday, December 20, 2010 4:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Mg2+ or water 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 To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by MedImmune to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.
Re: [ccp4bb] Mg2+ or water
I agree. It is very unlikely to be Magnesium ion; may be an ordered water! I'd recommend to have a look at the following paper which discusses the different properties of Mg2+, Mn2+, and Zn2+. Charles W. Bock, Amy Kaufman Katz, George D. Markham, and Jenny P. Glusker. Manganese as a replacement for Magnesium and Zinc: Functional comparison of the divalent ions. (J. Am. Chem. Soc. 1999, 121, 7360-7372) Ibrahim On 12/20/10 6:14 PM, Dima Klenchin klenc...@facstaff.wisc.edu wrote: Sorry, the attachment is in here. Doesn't look like Mg2+ at all. Distances are too long, Mg is never coordinated by amides and if it were Mg you would have seen waters around it. Looks like tightly bound water to me. - Dima On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu mailto:jlliu20022...@gmail.comjlliu20022...@gmail.com 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 Content-type: image/png; name=367-mgtest.png Content-disposition: attachment; filename=367-mgtest.png X-Attachment-Id: f_ghy0k5e31
Re: [ccp4bb] Mg2+ or water
Hi, I'm not sure if it has been mentioned yet, but you could take an experimental approach if you still have crystals. You could soak them with EDTA/EGTA and if the density disappears that is good evidence it was Mg (or other divalent cation), if not then putatively water. You could also soak with Mn (assuming the Mn will bind the Mg site) and look for anomolous signal. John
Re: [ccp4bb] Mg2+ or water
Another option would be to collect data at the Mn K edge (1.89A) - at this wavelength Mg has a weak anomalous signal that you should still be able to detect. I've used Mn K edge to successfully distinguish between Mg, Mn and Ca ions as well as identify them as ions and not waters by looking at peaks in the anomalous maps since peak intensity relates to anomalous signal arising from different ions at different wavelengths. For details, see: http://scripts.iucr.org/cgi-bin/paper?S0907444904026800 http://www.cell.com/structure/retrieve/pii/S0969212604000243 On 21 December 2010 15:04, John Bruning jbrun...@gmail.com wrote: Hi, I'm not sure if it has been mentioned yet, but you could take an experimental approach if you still have crystals. You could soak them with EDTA/EGTA and if the density disappears that is good evidence it was Mg (or other divalent cation), if not then putatively water. You could also soak with Mn (assuming the Mn will bind the Mg site) and look for anomolous signal. John
Re: [ccp4bb] Mg2+ or water
On Dec 20, 2010, at 1:16 PM, jlliu liu wrote: it is also within hydrogen bonding distance to the main chain N of another protein residue. This also strongly suggests it is not Mg2+, which prefers hard ligands such as charged oxygen, rather than softer ligands like uncharged backbone nitrogens (the interactions are primarily electrostatic, rather than orbital-mediated).
Re: [ccp4bb] Mg2+ or water
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
Re: [ccp4bb] Mg2+ or water
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 + 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 ***
Re: [ccp4bb] Mg2+ or water
If it's more than likely Mg and it's easy to grow crystals, try soaking/cogrowing BaCl2/BaOAc. At least in the RNA world, Mg sites can easily be displaced by Ba. The latter of course has anomalous signal on the home sources. Place your divalents using the anomalous diff map. Have no clue what this .odp file ext is so I can't view the png. F On Dec 20, 2010, at 2:16 PM, 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 - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Re: [ccp4bb] Mg2+ or water
On 20/12/10 21:48, Robbie Joosten wrote: 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. I tend to agree with Robbie. I wonder what WASP would say... (if you use Coot, you can try the Highly Coordinated Waters validation test - a symmetry-enhanced implementation of the Nayal Di Cera (1996) algorithm). Paul.
Re: [ccp4bb] Mg2+ or water
Sorry, the attachment is in here. Doesn't look like Mg2+ at all. Distances are too long, Mg is never coordinated by amides and if it were Mg you would have seen waters around it. Looks like tightly bound water to me. - Dima On Mon, Dec 20, 2010 at 4:16 PM, jlliu liu mailto:jlliu20022...@gmail.comjlliu20022...@gmail.com 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 Content-type: image/png; name=367-mgtest.png Content-disposition: attachment; filename=367-mgtest.png X-Attachment-Id: f_ghy0k5e31
