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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
>
>
>