115d
From Proteopedia
(New page: 200px<br /><applet load="115d" size="450" color="white" frame="true" align="right" spinBox="true" caption="115d, resolution 1.700Å" /> '''ORDERED WATER STRUC...) |
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| - | [[Image:115d.gif|left|200px]]<br /><applet load="115d" size=" | + | [[Image:115d.gif|left|200px]]<br /><applet load="115d" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="115d, resolution 1.700Å" /> | caption="115d, resolution 1.700Å" /> | ||
'''ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION'''<br /> | '''ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was | + | The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer. |
==About this Structure== | ==About this Structure== | ||
| - | 115D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 115D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=115D OCA]. |
==Reference== | ==Reference== | ||
Ordered water structure in an A-DNA octamer at 1.7 A resolution., Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D, J Biomol Struct Dyn. 1986 Feb;3(4):623-47. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3271041 3271041] | Ordered water structure in an A-DNA octamer at 1.7 A resolution., Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D, J Biomol Struct Dyn. 1986 Feb;3(4):623-47. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=3271041 3271041] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Cruse, W | + | [[Category: Cruse, W B.T.]] |
[[Category: Kennard, O.]] | [[Category: Kennard, O.]] | ||
[[Category: Nachman, J.]] | [[Category: Nachman, J.]] | ||
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[[Category: modified]] | [[Category: modified]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:37:37 2008'' |
Revision as of 09:37, 21 February 2008
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ORDERED WATER STRUCTURE IN AN A-DNA OCTAMER AT 1.7 ANGSTROMS RESOLUTION
Overview
The crystal structure of the deoxyoctamer d(G-G-Br U-A-BrU-A-C-C) was refined to a resolution of 1.7 A using combined diffractometer and synchrotron data. The analysis was carried out independently in two laboratories using different procedures. Although the final results are identical the comparison of the two approaches highlights potential problems in the refinement of oligonucleotides when only limited data are available. As part of the analysis the positions of 84 solvent molecules in the asymmetric unit were established. The DNA molecule is highly solvated, particularly the phosphate-sugar back-bone and the functional groups of the bases. The major groove contains, in the central BrU-A-BrU-A region, a ribbon of water molecules forming closed pentagons with shared edges. These water molecules are linked to the base O and N atoms and to the solvent chains connecting the O-1 phosphate oxygen atoms on each strand. The minor groove is also extensively hydrated with a continuous network in the central region and other networks at each end. The pattern of hydration is briefly compared with that observed in the structure of a B-dodecamer.
About this Structure
115D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Ordered water structure in an A-DNA octamer at 1.7 A resolution., Kennard O, Cruse WB, Nachman J, Prange T, Shakked Z, Rabinovich D, J Biomol Struct Dyn. 1986 Feb;3(4):623-47. PMID:3271041
Page seeded by OCA on Thu Feb 21 11:37:37 2008
