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RE: [ccp4bb]: Mystery molecule



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David,

Your "mystery molecule" is citric acid (two of them) coordinating a metal
ion!

Dave
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 David Borhani, Ph.D.
 Senior Research Chemist I
 Southern Research Institute		Tel:	(205) 581-2555
 2000 Ninth Avenue South		Fax:	(205) 581-2877
 Birmingham, AL 35205 USA		E-mail:	borhani@sri.org
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

> ----------
> From: 	david lawson[SMTP:david.lawson@bbsrc.ac.uk]
> Sent: 	Monday, 12 June 2000 09:10
> To: 	'ccp4bb@dl.ac.uk'
> Subject: 	[ccp4bb]: Mystery molecule
> 
> <<File: unk.bmp>>
> Dear All,
> 
> We have refined a structure at 1.35 A resolution and identified an unusual
> ligand bound to the protein. It is clearly defined in the density enabling
> us to make a good structural template by driving waters into the density.
> Using this template we have searched the Beilstein chemical database and
> come up with one very convincing hit. The chemical name is:
> 
> (2,7,7-carboxymethyl-3,8-dioxo-1,4,6,9-tetraoxa-5lambda5-phosphaspiro[4.4]
> no
> n-2-yl)-acetic acid - I don't know if there is a trivial name.
> 
> The empirical formula is C12,H13,O14,P and the Beilstein registry number
> is
> 6455461.
> 
> This structure fits the density well and here are the refined coordinates:
> 
> ATOM   1422  O1  UNK A 301      24.489  -0.984  19.022  1.00 22.34
> O
> ATOM   1423  C2  UNK A 301      23.495  -1.864  19.032  1.00 23.72
> C
> ATOM   1424  C3  UNK A 301      23.474  -2.755  20.240  1.00 23.07
> C
> ATOM   1425  O4  UNK A 301      24.402  -2.209  21.110  1.00 21.47
> O
> ATOM   1426  P5  UNK A 301      25.128  -1.034  20.485  1.00 29.61
> P
> ATOM   1427  O6  UNK A 301      25.314   0.467  20.915  1.00 23.72
> O
> ATOM   1428  C7  UNK A 301      26.694   0.790  20.920  1.00 24.76
> C
> ATOM   1429  C8  UNK A 301      27.455  -0.443  20.386  1.00 21.71
> C
> ATOM   1430  O9  UNK A 301      26.623  -1.443  20.066  1.00 19.40
> O
> ATOM   1431  O10 UNK A 301      28.678  -0.511  20.284  1.00 19.79
> O
> ATOM   1432  O11 UNK A 301      22.669  -1.927  18.101  1.00 24.08
> O
> ATOM   1433  C12 UNK A 301      23.723  -4.165  19.842  1.00 23.86
> C
> ATOM   1434  C13 UNK A 301      23.596  -5.099  21.023  1.00 27.64
> C
> ATOM   1435  C14 UNK A 301      22.100  -2.525  20.918  1.00 25.22
> C
> ATOM   1436  C15 UNK A 301      21.709  -1.168  21.329  1.00 26.15
> C
> ATOM   1437  O16 UNK A 301      22.045  -0.147  20.750  1.00 22.68
> O
> ATOM   1438  O17 UNK A 301      22.649  -5.958  21.141  1.00 29.96
> O
> ATOM   1439  O18 UNK A 301      24.491  -4.970  21.910  1.00 25.74
> O
> ATOM   1440  C19 UNK A 301      27.227   1.229  22.278  1.00 22.92
> C
> ATOM   1441  C20 UNK A 301      27.205   0.165  23.320  1.00 21.07
> C
> ATOM   1442  O21 UNK A 301      27.179   0.523  24.602  1.00 21.16
> O
> ATOM   1443  O22 UNK A 301      27.178  -1.106  23.119  1.00 21.36
> O
> ATOM   1444  C23 UNK A 301      26.898   1.829  19.812  1.00 26.81
> C
> ATOM   1445  C24 UNK A 301      26.308   3.195  19.991  1.00 31.63
> C
> ATOM   1446  O25 UNK A 301      27.097   4.152  20.360  1.00 34.60
> O
> ATOM   1447  O26 UNK A 301      25.046   3.394  19.772  1.00 34.94
> O
> ATOM   1448  O27 UNK A 301      20.967  -1.055  22.351  1.00 26.36
> O
> 
> A bitmat image is also attached (this can be read into Word and Powerpoint
> and probably several other packages).
> 
> It doesn't look like any 'natural' ligand and may perhaps be some kind of
> chelator. Incidently we used the 'EDTA-free Complete' protease inhibitor
> cocktail during protein preparation. However, Roche say this is not an
> ingredient. 
> 
> Has anyone seen this molecule before? If so does it have a trivial name
> and
> where is it likely to have come from?
> 
> Thanks in advance,
> 
> Dave Lawson
> 
> -------------------------------
> 
> Dr. David M. Lawson
> Biological Chemistry Dept.,
> John Innes Centre,
> Norwich,
> NR4 7UH, UK.
> Tel: +44-(0)1603-450725
> Fax: +44-(0)1603-450018
> Email: david.lawson@bbsrc.ac.uk
>  
> 
>