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| - | [[Image:260d.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II== |
| - | |PDB= 260d |SIZE=350|CAPTION= <scene name='initialview01'>260d</scene>, resolution 1.900Å
| + | <StructureSection load='260d' size='340' side='right'caption='[[260d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <table><tr><td colspan='2'>[[260d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=260D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=260D FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=260d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=260d OCA], [https://pdbe.org/260d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=260d RCSB], [https://www.ebi.ac.uk/pdbsum/260d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=260d ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=260d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=260d OCA], [http://www.ebi.ac.uk/pdbsum/260d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=260d RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Ban C]] |
| - | '''CRYSTAL STRUCTURE OF THE SELF-COMPLEMENTARY 5'-PURINE START DECAMER D(GCACGCGTGC) IN THE A-DNA CONFORMATION-PART II'''
| + | [[Category: Sundaralingam M]] |
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| - | | + | |
| - | ==Overview==
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| - | 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.
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| - | ==About this Structure==
| + | |
| - | 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].
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| - | ==Reference==
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| - | 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]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Ban, C.]] | + | |
| - | [[Category: Sundaralingam, M.]] | + | |
| - | [[Category: a-dna]]
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| - | [[Category: double helix]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:45:34 2008''
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