260d
From Proteopedia
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| - | [[Image:260d.gif|left|200px]] | + | [[Image:260d.gif|left|200px]] |
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| - | '''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II''' | + | {{Structure |
| + | |PDB= 260d |SIZE=350|CAPTION= <scene name='initialview01'>260d</scene>, resolution 1.900Å | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
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| + | '''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II''' | ||
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==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 260D is a [ | + | 260D is a [[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=260D OCA]. |
==Reference== | ==Reference== | ||
| - | Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:[http:// | + | Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8873996 8873996] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Ban, C.]] | [[Category: Ban, C.]] | ||
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[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:43:19 2008'' |
Revision as of 13:43, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II
Overview
The crystal structure of the alternating 5'-purine start decamer d(GCGCGCGCGC) was found to be in the left-handed Z-DNA conformation. Inasmuch as the A.T base pair is known to resist Z-DNA formation, we substituted A.T base pairs in the dyad-related positions of the decamer duplex. The alternating self-complementary decamer d(GCACGCGTGC) crystallizes in a different hexagonal space group, P6(1)22, with very different unit cell dimensions a = b = 38.97 and c = 77.34 A compared with the all-G.C alternating decamer. The A.T-containing decamer has one strand in the asymmetric unit, and because it is isomorphous to some other A-DNA decamers it was considered also to be right-handed. The structure was refined, starting with the atomic coordinates of the A-DNA decamer d(GCGGGCCCGC), by use of 2491 unique reflections out to 1.9-A resolution. The refinement converged to an R value of 18.6% for a total of 202 nucleotide atoms and 32 water molecules. This research further demonstrates that A.T base pairs not only resist the formation of Z-DNA but can also assist the formation of A-DNA by switching the helix handedness when the oligomer starts with a 5'-purine; also, the length of the inner Z-DNA stretch (d(CG)n) is reduced from an octamer to a tetramer. It may be noted that these oligonucleotide properties are in crystals and not necessarily in solutions.
About this Structure
260D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of the self-complementary 5'-purine start decamer d(GCACGCGTGC) in the A-DNA conformation. II., Ban C, Sundaralingam M, Biophys J. 1996 Sep;71(3):1222-7. PMID:8873996
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