432d

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(New page: 200px<br /><applet load="432d" size="350" color="white" frame="true" align="right" spinBox="true" caption="432d, resolution 1.89&Aring;" /> '''D(GGCCAATTGG) COMPLE...)
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==Overview==
==Overview==
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The single-crystal X-ray structure of the complex between the minor groove, binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a, novel way of off-centered binding, with an unique hydrogen bond between, the minor groove binder and a CG base pair. Application of crystal, engineering and cryocooling techniques helped to extend the resolution to, 1.9 A, resulting in an unambiguous determination of drug conformation and, orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o), &gt; 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on, guanine is believed to prevent drug binding in the minor groove, the, nature and stability of the CG-DAPI contact was further addressed in full, detail using ab initio quantum chemical methods. The amino groups involved, in the guanine-drug interaction are substantially nonplanar, resulting in, an energy gain of about 5 kcal/mol. The combined structural and, theoretical data suggest that the guanine NH(2)-group does not destabilize, the drug binding to an extent that it prevents complexation.
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The single-crystal X-ray structure of the complex between the minor groove binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a novel way of off-centered binding, with an unique hydrogen bond between the minor groove binder and a CG base pair. Application of crystal engineering and cryocooling techniques helped to extend the resolution to 1.9 A, resulting in an unambiguous determination of drug conformation and orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o) &gt; 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on guanine is believed to prevent drug binding in the minor groove, the nature and stability of the CG-DAPI contact was further addressed in full detail using ab initio quantum chemical methods. The amino groups involved in the guanine-drug interaction are substantially nonplanar, resulting in an energy gain of about 5 kcal/mol. The combined structural and theoretical data suggest that the guanine NH(2)-group does not destabilize the drug binding to an extent that it prevents complexation.
==About this Structure==
==About this Structure==
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Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10600105 10600105]
Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10600105 10600105]
[[Category: Protein complex]]
[[Category: Protein complex]]
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[[Category: Meervelt, L.Van.]]
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[[Category: Meervelt, L Van.]]
[[Category: Vlieghe, D.]]
[[Category: Vlieghe, D.]]
[[Category: DAP]]
[[Category: DAP]]
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[[Category: triplet formation]]
[[Category: triplet formation]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 21:43:15 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:12:11 2008''

Revision as of 17:12, 21 February 2008

Image:432d.gif

432d, resolution 1.89Å

Drag the structure with the mouse to rotate

D(GGCCAATTGG) COMPLEXED WITH DAPI

Overview

The single-crystal X-ray structure of the complex between the minor groove binder 4',6-diamidino-2-phenylindole (DAPI) and d(GGCCAATTGG) reveals a novel way of off-centered binding, with an unique hydrogen bond between the minor groove binder and a CG base pair. Application of crystal engineering and cryocooling techniques helped to extend the resolution to 1.9 A, resulting in an unambiguous determination of drug conformation and orientation. The structure was refined to completion using SHELXL-93, resulting in a residual factor R of 18. 0% for 3562 reflections with F(o) > 4sigma(F(o)) including 81 water molecules. As the bulky NH(2)-group on guanine is believed to prevent drug binding in the minor groove, the nature and stability of the CG-DAPI contact was further addressed in full detail using ab initio quantum chemical methods. The amino groups involved in the guanine-drug interaction are substantially nonplanar, resulting in an energy gain of about 5 kcal/mol. The combined structural and theoretical data suggest that the guanine NH(2)-group does not destabilize the drug binding to an extent that it prevents complexation.

About this Structure

432D is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.

Reference

Crystal structure of d(GGCCAATTGG) complexed with DAPI reveals novel binding mode., Vlieghe D, Sponer J, Van Meervelt L, Biochemistry. 1999 Dec 14;38(50):16443-51. PMID:10600105

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