1ue3: Difference between revisions

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{{Seed}}
[[Image:1ue3.png|left|200px]]


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==Crystal structure of d(GCGAAAGC) containing hexaamminecobalt==
The line below this paragraph, containing "STRUCTURE_1ue3", creates the "Structure Box" on the page.
<StructureSection load='1ue3' size='340' side='right'caption='[[1ue3]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)  
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ue3]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UE3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UE3 FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
{{STRUCTURE_1ue3|  PDB=1ue3  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ue3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ue3 OCA], [https://pdbe.org/1ue3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ue3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ue3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ue3 ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A DNA fragment d(GCGAAAGC), postulated to adopt a stable mini-hairpin structure on the basis of its extraordinary properties, has been X-ray analyzed. Two octamers related by a crystallographic twofold symmetry are aligned in an antiparallel fashion and associate to form a duplex, which is maintained by two Watson-Crick G.C base pairs and a subsequent sheared G.A pair at both ends. The central two A residues are free from base-pair formation. The corresponding base moieties of the two strands are intercalated and stacked on each other, forming a long column of G(1)-C(2)-G(3)-A(4)-A(5)(*)-A(5)-A(4)(*)-G(3)(*)-C(2)(*)-G(1)(*) (asterisks indicate the counter-strand). The Watson-Crick and major-groove sites of the four stacked adenine bases are exposed to the solvent region, suggesting a functional role. Since this structural motif is similar to those found in the nonamers d(G(Br)CGAAAGCT) and d(G(I)CGAAAGCT), the base-intercalated duplex may be a stable form of the specific sequence. Electrophoresis results suggest that the octamer has two states, monomeric and dimeric, in solution depending on the Mg(2+) concentration. The present duplex is preferred under the crystallization conditions, which correspond to physiologically allowed conditions.


===Crystal structure of d(GCGAAAGC) containing hexaamminecobalt===
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure.,Sunami T, Kondo J, Hirao I, Watanabe K, Miura KI, Takenaka A Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):90-6. Epub 2003 Dec, 18. PMID:14684897<ref>PMID:14684897</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 1ue3" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 14684897 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_14684897}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UE3 OCA].
[[Category: Hirao I]]
 
[[Category: Kondo J]]
==Reference==
[[Category: Miura K]]
Structure of d(GCGAAAGC) (hexagonal form): a base-intercalated duplex as a stable structure., Sunami T, Kondo J, Hirao I, Watanabe K, Miura KI, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2004 Jan;60(Pt 1):90-6. Epub 2003 Dec, 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14684897 14684897]
[[Category: Sunami T]]
[[Category: Hirao, I.]]
[[Category: Takenaka A]]
[[Category: Kondo, J.]]
[[Category: Watanabe K]]
[[Category: Miura, K.]]
[[Category: Sunami, T.]]
[[Category: Takenaka, A.]]
[[Category: Watanabe, K.]]
[[Category: Base-intercalated duplex]]
[[Category: Dna]]
[[Category: Mini-hairpin structure]]
[[Category: Sheared g:a pair]]
[[Category: Zipper-like duplex]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Jul 27 19:49:05 2008''

Latest revision as of 06:05, 5 July 2023

Crystal structure of d(GCGAAAGC) containing hexaamminecobalt

1ue3, resolution 2.15Å

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