tag:blogger.com,1999:blog-37148773.post8335678277040735229..comments2024-03-27T14:50:47.345-04:00Comments on <center>Sandwalk</center>: Monday's Molecule #156Larry Moranhttp://www.blogger.com/profile/05756598746605455848noreply@blogger.comBlogger12125tag:blogger.com,1999:blog-37148773.post-34477048891904222562012-01-26T17:41:39.864-05:002012-01-26T17:41:39.864-05:00Sweet!Sweet!Nostranoodlehttps://www.blogger.com/profile/04808159695811673848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-54254288953993175242012-01-25T17:41:13.695-05:002012-01-25T17:41:13.695-05:00You are correct. The His and homocitrate structure...You are correct. The His and homocitrate structures are not correct.<br /><br />You could share the prize except that you used a pseudonym. You get the "pedantic anonymous chemist" award as a consolation prize. :-)Larry Moranhttps://www.blogger.com/profile/05756598746605455848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-74641645039790478022012-01-25T02:39:51.224-05:002012-01-25T02:39:51.224-05:00The atom liganding Fe2-7 is a carbon, not a nitrog...<i>The atom liganding Fe2-7 is a carbon, not a nitrogen as previously thought.</i><br /><br />That's really cool! Discrimination between N and C at 1.0A resolution is very nice. I didn't think it's going to be convincing but it is, in fact, almost rock solid.DKnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-68152456257981349532012-01-24T17:55:42.843-05:002012-01-24T17:55:42.843-05:00Look carefully guys, the textbook ligand is homoci...Look carefully guys, the textbook ligand is homocitrate, but theres no homocitrate in the structure above. Count the atoms on the right hand side, its C2H2O3 (glycolic acid doubly deprotonated) and C3H4N2 (imidazole) as I stated above.<br /><br />(btw I cant make the lunch date, but Ill happily accept any "Pedantic Chemist is Boring yet Technically Correct" awards you happen to have lying around)Nostranoodlehttps://www.blogger.com/profile/04808159695811673848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22603817138348431302012-01-24T13:50:23.971-05:002012-01-24T13:50:23.971-05:00OK, no one is stepping up, so I'll take a try:...OK, no one is stepping up, so I'll take a try: it is the iron-molybdenum cofactor (FeMoco) of the nitrogenase enyme that Azotobacter vinelandii uses to fixes atmospheric nitrogen gas into ammonia, thus making nitrogen biologically available for most other species. The carbon-containing structures off the molybdenum are homocitrate and histidine ligands. The atom surrounded by irons was recently unambiguously identified as carbon; previously, it was thought that it could have been nitrogen or oxygen.Thomas Ferrarohttps://www.blogger.com/profile/04197195813012515736noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-88531196041424911562012-01-24T13:40:31.038-05:002012-01-24T13:40:31.038-05:00It is the Iron Molybdenum cofactor (FeMo-cofactor)...It is the Iron Molybdenum cofactor (FeMo-cofactor) of the MoFe-protein, part of the active site of nitrogenase. The organic part is homocitrate. It was thought that the small central atom was nitrogen (before that, a paper from 1992 referred to it as a "bridging ligand"), but is now known to be carbon.Matt Ghttps://www.blogger.com/profile/07745943486966305844noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-22518066916869870232012-01-24T00:17:58.583-05:002012-01-24T00:17:58.583-05:00Being sadly ignorant of biochemisty (indeed, of ch...Being sadly ignorant of biochemisty (indeed, of chemistry as it's been a long long time since first year), I've no hope of determining the actual molecule. But I remember comment that in the early earth Molybdenum might have been a limiting factor in the growth of eukaryotic life, as it is needed for fixing nitrogen. After a little google-cheating I conclude that the above is a nitrogenase.<br /><br />William HydeAnonymousnoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-53955612969943464742012-01-24T00:06:34.463-05:002012-01-24T00:06:34.463-05:00Looks like the FeMoco cofactor from the nitrogenas...Looks like the FeMoco cofactor from the nitrogenase enzyme, but the ligands are all truncated (HS instead of Cys, glycolic acid instead of homocitric, and imidazole in place of His) as though someone isolated it for Xray crystallography. The difference would be the carbon atom as the central ligand in the middle of the iron atoms, instead of nitrogen as previously reported?Nostranoodlehttps://www.blogger.com/profile/04808159695811673848noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-62151229799184363492012-01-23T22:41:11.276-05:002012-01-23T22:41:11.276-05:00Molecule # 156 is the molybdenum nitrogenase cofac...Molecule # 156 is the molybdenum nitrogenase cofactor, on which all the ecosphere relies for the bulk of its nitrogen fixation. The new discovery is the fact that it contains a central "interstitial" carbon atom. As for the white carbon atoms, from this perspective, all we can say is that it contains an imidazole ring. Although histidine (which contains an imidazole ring) is cited as a ligand for the molybdenum atom in this molecule (along with homocitrate), one can not be sure, from the structure shown, about how they are bound to the other atoms. Besides, if it were histidine, it should contain one more carbon and one more nitrogen atom.Raul A. FĂ©lix de Sousanoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-35483072037706666942012-01-23T15:57:29.203-05:002012-01-23T15:57:29.203-05:00The iron-molybdenum cofactor of the nitrogenase co...The iron-molybdenum cofactor of the nitrogenase complex - required for the entry of molecular nitrogen into the biosphere<br /><br />The part with the white atoms is homocitrate (according to Lehninger 5th ed).<br /><br />Difference? Compared to the structure given in Lehninger 5th edition, this molecule has an SH-group attached to the left hand side in the diagram (a total of 10 rather than 9 S).Unknownhttps://www.blogger.com/profile/09160581643157925453noreply@blogger.comtag:blogger.com,1999:blog-37148773.post-12887442693898248022012-01-23T13:10:41.591-05:002012-01-23T13:10:41.591-05:00That is the FeMo cofactor of nitrogenase.
"...That is the FeMo cofactor of nitrogenase. <br /><br />"the FeMo cofactor, is a [Mo:7Fe:9S:X]:homocitrate cluster, the largest and most complex biological metal center known to date." (from reference 1 cited below)<br /><br />The white carbons belong to 3-HYDROXY-3-CARBOXY-ADIPIC ACID (homocitrate); except for those in a ring with the two nitrogens, which belong to a histidine residue of the protein.<br /><br /><br />The atom liganding Fe2-7 is a carbon, not a nitrogen as previously thought.<br /><br />1)<br />T. Spatzal, et al, "Evidence for Interstitial Carbon in Nitrogenase FeMo Cofactor"<br />Science 18 November 2011:<br />Vol. 334 no. 6058 p. 940<br />DOI: 10.1126/science.1214025<br /><br />Abstract: "The identity of the interstitial light atom in the center of the FeMo cofactor of nitrogenase has been enigmatic since its discovery. Atomic-resolution x-ray diffraction data and an electron spin echo envelope modulation (ESEEM) analysis now provide direct evidence that the ligand is a carbon species."<br /><br />2)<br />K.M. Lancaster, et al. "X-ray Emission Spectroscopy Evidences a Central Carbon in the Nitrogenase Iron-Molybdenum Cofactor"<br />Science 18 November 2011:<br />Vol. 334 no. 6058 pp. 974-977<br />DOI: 10.1126/science.1206445David J. Schullernoreply@blogger.comtag:blogger.com,1999:blog-37148773.post-41147898448487382142012-01-23T12:22:16.660-05:002012-01-23T12:22:16.660-05:00Iron-Molybdenum-Sulfur-Homocitrate cluster from so...Iron-Molybdenum-Sulfur-Homocitrate cluster from some nitrogenease, obviously. I am guessing the error has something to do with citrate stereochemistry but I don't have time today for googling and figuring it out.Dima Klenchinnoreply@blogger.com