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| [[Image:314d.gif|left|200px]]
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| {{Structure
| | ==Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR== |
| |PDB= 314d |SIZE=350|CAPTION= <scene name='initialview01'>314d</scene>, resolution 1.900Å
| | <StructureSection load='314d' size='340' side='right'caption='[[314d]], [[Resolution|resolution]] 1.90Å' scene=''> |
| |SITE= | | == Structural highlights == |
| |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</scene>
| | <table><tr><td colspan='2'>[[314d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=314D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=314D 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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> |
| }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=314d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=314d OCA], [https://pdbe.org/314d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=314d RCSB], [https://www.ebi.ac.uk/pdbsum/314d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=314d ProSAT]</span></td></tr> |
| | </table> |
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| '''Z-DNA HEXAMER WITH 5' OVERHANGS THAT FORM A REVERSE WOBBLE BASE PAIR'''
| | ==See Also== |
| | | *[[Z-DNA|Z-DNA]] |
| | | __TOC__ |
| ==Overview== | | </StructureSection> |
| We have solved the structures of the homoduplex d(Gm5CGCGCG)2, and the heteroduplexes d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG). The structures form six base-pairs of identical Z-DNA duplexes with single nucleotides overhanging at the 5'-ends. The overhanging nucleotide from one strand remains stacked and sandwiched between the blunt-ends of two adjacent Z-DNA duplexes, while the overhanging base of the opposing strand is extra-helical. The stacked and the extra-helical bases from adjacent duplexes pair to form a distorted d(G x G) reverse Hoogsteen base-pair in the d(Gm5CGCGCG)2 homoduplex, and d(G x T) reverse wobble and d(G x C) reverse Watson-Crick base-pairs in the d(GCGCGCG)/d(TCGCGCG) and d(GCGCGCG)/d(CCGCGCG) heteroduplexes, respectively. Interestingly, only the d(G,T) and d(G x C) base-pairs were observed in the heteroduplexes, suggesting that both the d(G x T) reverse wobble and d(G x C) reverse Watson-Crick base-pairs are more stable in this crystal environment than the d(G x G) reverse Hoogsteen base-pair. To estimate the relative stability of the three types of reverse base-pairs, crystals were grown using various mixtures of sequences and their strand compositions analyzed by mass spectrometry. The d(G x C) reverse Watson-Crick base-pair was estimated to be more stable by approximately 1.5 kcal/mol and the d(G x T) reverse wobble base-pair more stable by approximately 0.5 kcal/mol than the d(G x G) reverse Hoogsteen base-pair. The step during crystallization responsible for discriminating between the strands in the crystal is highly cooperative, suggesting that it occurs during the initial nucleating event of crystal growth.
| | [[Category: Large Structures]] |
| | | [[Category: Eichman BF]] |
| ==About this Structure==
| | [[Category: Ho PS]] |
| 314D 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=314D OCA].
| | [[Category: Mooers BHM]] |
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| ==Reference==
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| The structures and relative stabilities of d(G x G) reverse Hoogsteen, d(G x T) reverse wobble, and d(G x C) reverse Watson-Crick base-pairs in DNA crystals., Mooers BH, Eichman BF, Ho PS, J Mol Biol. 1997 Jun 27;269(5):796-810. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9223642 9223642]
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| [[Category: Protein complex]] | |
| [[Category: Eichman, B F.]] | |
| [[Category: Ho, P S.]] | |
| [[Category: Mooers, B H.M.]] | |
| [[Category: MG]]
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| [[Category: NCO]]
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| [[Category: double helix]]
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| [[Category: flipped-out base]]
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| [[Category: overhanging base]]
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| [[Category: z-dna]]
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| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:54:31 2008''
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