Re: [ccp4bb] Lithium versus Sodium
Dear Matt, We were working with Hal2p a lithium inhibited Ins-mono-PPase like protein 10 years ago. We had good biochemistry showing that lithium replaced mg at the active site. We grow crystals in presence of Li and we worked with 1.6 A diffraction data. Unfortunatelly we did not see any electron density peak, however, the "Li" site displayed nice tetrahedral coordination having four oxygen atoms as ligands. Armando El 12/01/2012, a las 18:16, Matthew Franklin escribió: > Hi Ed - > > There was a peak in the difference maps, as I recall. I believe it initially > got built as a water, but that proved to be too many electrons, giving a > negative peak. I removed the water, but it was clear that something needed > to be there, at which point I started casting about for alternative atoms, > and settled on lithium. I'm pretty sure I never tried to put sodium in there > and see if it refined. > > Caveat: this work was all done eight years ago, and I don't have access to > any of the files anymore. So I can't verify any of these statements! > However, I did deposit Fobs for these structures, if you care to make your > own maps... > > I just checked the structure in EDS, and the peak for the lithium is pretty > low, around 0.6 sigma. I would say that it looked better in the maps I was > using. > > Hope that helps, > Matt > > > On 1/12/12 11:22 AM, Ed Pozharski wrote: >> Matt, >> >> thank you, this is an excellent summary. One question remains - the >> lithium peak should be, afaiu, much lower than the water/sodium. Was >> there a peak in difference map or was placement based on identifying >> something that looked like a coordination site? >> >> Cheers, >> >> Ed. >> >> On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote: >>> On 1/12/12 9:42 AM, Ed Pozharski wrote: On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: > Do you have ultra-high resolution? Something I did not…. Are there > many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI 39 in total. Some are fairly low resolution (2.8A), and only five are higher than 1.2A. I'd think that placing lithium ion should be based on some extra-crystallographic evidence, plus maybe some structural considerations such as correctly placed coordinating ligands. >>> Since I'm responsible for eight of those structures, I'll just say that >>> I thought fairly hard before building a lithium into that peak, knowing >>> that I couldn't really distinguish it from water or sodium. I was >>> working with a 1.7 A map, and I put the lithium there based on three >>> criteria: >>> >>> - the crystals grew in something like 2 M lithium sulfate, whereas the >>> only source of sodium would have been from the buffer or the protein >>> solution >>> >>> - there were two negatively charged residues coordinating the peak in >>> question, suggesting it was a cation >>> >>> - the bond distances were consistent with lithium coordination, for what >>> that's worth at this resolution >>> >>> That was the first structure (1TW7), and all of the others were treated >>> the same since it was the same crystals soaked with different compounds >>> in the same conditions. >>> >>> - Matt >>> >>> > > > -- > Matthew Franklin, Ph. D. > Senior Research Scientist > New York Structural Biology Center > 89 Convent Avenue, New York, NY 10027 > (646) 275-7165
Re: [ccp4bb] Lithium versus Sodium
Hi Ed - There was a peak in the difference maps, as I recall. I believe it initially got built as a water, but that proved to be too many electrons, giving a negative peak. I removed the water, but it was clear that something needed to be there, at which point I started casting about for alternative atoms, and settled on lithium. I'm pretty sure I never tried to put sodium in there and see if it refined. Caveat: this work was all done eight years ago, and I don't have access to any of the files anymore. So I can't verify any of these statements! However, I did deposit Fobs for these structures, if you care to make your own maps... I just checked the structure in EDS, and the peak for the lithium is pretty low, around 0.6 sigma. I would say that it looked better in the maps I was using. Hope that helps, Matt On 1/12/12 11:22 AM, Ed Pozharski wrote: Matt, thank you, this is an excellent summary. One question remains - the lithium peak should be, afaiu, much lower than the water/sodium. Was there a peak in difference map or was placement based on identifying something that looked like a coordination site? Cheers, Ed. On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote: On 1/12/12 9:42 AM, Ed Pozharski wrote: On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: Do you have ultra-high resolution? Something I did not…. Are there many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI 39 in total. Some are fairly low resolution (2.8A), and only five are higher than 1.2A. I'd think that placing lithium ion should be based on some extra-crystallographic evidence, plus maybe some structural considerations such as correctly placed coordinating ligands. Since I'm responsible for eight of those structures, I'll just say that I thought fairly hard before building a lithium into that peak, knowing that I couldn't really distinguish it from water or sodium. I was working with a 1.7 A map, and I put the lithium there based on three criteria: - the crystals grew in something like 2 M lithium sulfate, whereas the only source of sodium would have been from the buffer or the protein solution - there were two negatively charged residues coordinating the peak in question, suggesting it was a cation - the bond distances were consistent with lithium coordination, for what that's worth at this resolution That was the first structure (1TW7), and all of the others were treated the same since it was the same crystals soaked with different compounds in the same conditions. - Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165
Re: [ccp4bb] Lithium versus Sodium
Matt, thank you, this is an excellent summary. One question remains - the lithium peak should be, afaiu, much lower than the water/sodium. Was there a peak in difference map or was placement based on identifying something that looked like a coordination site? Cheers, Ed. On Thu, 2012-01-12 at 10:23 -0500, Matthew Franklin wrote: > On 1/12/12 9:42 AM, Ed Pozharski wrote: > > On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: > >> Do you have ultra-high resolution? Something I did not…. Are there > >> many examples in the pdb of proteins with Li+ refined? > > http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI > > > > 39 in total. Some are fairly low resolution (2.8A), and only five are > > higher than 1.2A. I'd think that placing lithium ion should be based on > > some extra-crystallographic evidence, plus maybe some structural > > considerations such as correctly placed coordinating ligands. > > > Since I'm responsible for eight of those structures, I'll just say that > I thought fairly hard before building a lithium into that peak, knowing > that I couldn't really distinguish it from water or sodium. I was > working with a 1.7 A map, and I put the lithium there based on three > criteria: > > - the crystals grew in something like 2 M lithium sulfate, whereas the > only source of sodium would have been from the buffer or the protein > solution > > - there were two negatively charged residues coordinating the peak in > question, suggesting it was a cation > > - the bond distances were consistent with lithium coordination, for what > that's worth at this resolution > > That was the first structure (1TW7), and all of the others were treated > the same since it was the same crystals soaked with different compounds > in the same conditions. > > - Matt > > -- Oh, suddenly throwing a giraffe into a volcano to make water is crazy? Julian, King of Lemurs
Re: [ccp4bb] Lithium versus Sodium
On 1/12/12 9:42 AM, Ed Pozharski wrote: On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: Do you have ultra-high resolution? Something I did not…. Are there many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI 39 in total. Some are fairly low resolution (2.8A), and only five are higher than 1.2A. I'd think that placing lithium ion should be based on some extra-crystallographic evidence, plus maybe some structural considerations such as correctly placed coordinating ligands. Since I'm responsible for eight of those structures, I'll just say that I thought fairly hard before building a lithium into that peak, knowing that I couldn't really distinguish it from water or sodium. I was working with a 1.7 A map, and I put the lithium there based on three criteria: - the crystals grew in something like 2 M lithium sulfate, whereas the only source of sodium would have been from the buffer or the protein solution - there were two negatively charged residues coordinating the peak in question, suggesting it was a cation - the bond distances were consistent with lithium coordination, for what that's worth at this resolution That was the first structure (1TW7), and all of the others were treated the same since it was the same crystals soaked with different compounds in the same conditions. - Matt -- Matthew Franklin, Ph. D. Senior Research Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (646) 275-7165
Re: [ccp4bb] Lithium versus Sodium
On Thu, 2012-01-12 at 09:52 +, Patel, Joe wrote: > Do you have ultra-high resolution? Something I did not…. Are there > many examples in the pdb of proteins with Li+ refined? http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcode=n/a&template=het2pdb.html¶m1=_LI 39 in total. Some are fairly low resolution (2.8A), and only five are higher than 1.2A. I'd think that placing lithium ion should be based on some extra-crystallographic evidence, plus maybe some structural considerations such as correctly placed coordinating ligands. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] Lithium versus Sodium
Hi Scott I may be completely wrong but I worked on a lithium and sodium inhibited enzyme during my PhD. At the time, it was considered that your chances of actually seeing density for a Li+ ion were slim to nil. Only 2 electrons makes them as tough as hydrogens. My efforts went into trying to prove I had a sodium ion bound over magnesium which is the catalytically active ion Do you have ultra-high resolution? Something I did not Are there many examples in the pdb of proteins with Li+ refined? Sorry no real help to you, but curious since it brings up old memories... Joe P Dr Joe Patel _ AstraZeneca Discovery Sciences, Structure & Biophysics UK 50S38, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG Tel +44 (0)1625 233543 Fax +44 (0)1625 230164 joe.pa...@astrazeneca.com <mailto:name.surn...@astrazeneca.com> P Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Scott Pegan Sent: 12 January 2012 06:10 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Lithium versus Sodium Hey all, Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry & Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254 -- AstraZeneca UK Limited is a company incorporated in England and Wales with registered number: 03674842 and a registered office at 2 Kingdom Street, London, W2 6BD. Confidentiality Notice: This message is private and may contain confidential, proprietary and legally privileged information. If you have received this message in error, please notify us and remove it from your system and note that you must not copy, distribute or take any action in reliance on it. Any unauthorised use or disclosure of the contents of this message is not permitted and may be unlawful. Disclaimer: Email messages may be subject to delays, interception, non-delivery and unauthorised alterations. Therefore, information expressed in this message is not given or endorsed by AstraZeneca UK Limited unless otherwise notified by an authorised representative independent of this message. No contractual relationship is created by this message by any person unless specifically indicated by agreement in writing other than email. Monitoring: AstraZeneca UK Limited may monitor email traffic data and content for the purposes of the prevention and detection of crime, ensuring the security of our computer systems and checking Compliance with our Code of Conduct and Policies.
[ccp4bb] Lithium versus Sodium
Hey all, Does anyone know of a good article that deals with differentiating between a lithium ion and sodium ion for density in a X-ray structures? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry & Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
