2p8d

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[[Image:2p8d.jpg|left|200px]]<br /><applet load="2p8d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2p8d, resolution 1.90&Aring;" />
 
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'''The Structure of the Dickerson Sequence with an Incorporated CeNA Residue'''<br />
 
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==Overview==
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==The Structure of the Dickerson Sequence with an Incorporated CeNA Residue==
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Cyclohexene nucleic acids (CeNA), which are characterized by the presence, of a cyclohexene moiety instead of a natural (deoxy)ribose sugar, are, known to increase the thermal and enzymatic stability when incorporated in, RNA oligonucleotides. As it has been demonstrated that even a single, cyclohexenyl nucleoside, when incorporated in an oligonucleotide, can have, a profound effect on the biological activity of the oligonucleotide, further research is warranted to study the complex of such, oligonucleotides with target proteins. In order to analyse the influence, of CeNA residues onto the helix conformation and hydration of natural, nucleic acid structures, a cyclohexenyl-adenine building block (xAr) was, incorporated into the Dickerson sequence CGCGA(xAr)TTCGCG. The crystal, structure of this sequence determined to a resolution of 1.90 A. The, global helix belongs to the B-type family and shows a water spine, which, is partially broken up by the apolar cyclohexene residue. The cyclohexene, ring adopts the (2)E-conformation allowing a better incorporation of the, residue in the dodecamer sequence. The crystal packing is stabilized by, cobalt hexamine residues and belongs to space group P222(1), never before, reported for nucleic acids.
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<StructureSection load='2p8d' size='340' side='right'caption='[[2p8d]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2p8d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P8D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2P8D FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#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=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=XAR:[(1R,4S,6S)-4-(6-AMINO-9H-PURIN-9-YL)-6-HYDROXYCYCLOHEX-2-EN-1-YL]METHYL+DIHYDROGEN+PHOSPHATE'>XAR</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2p8d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2p8d OCA], [https://pdbe.org/2p8d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2p8d RCSB], [https://www.ebi.ac.uk/pdbsum/2p8d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2p8d ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Cyclohexene nucleic acids (CeNA), which are characterized by the presence of a cyclohexene moiety instead of a natural (deoxy)ribose sugar, are known to increase the thermal and enzymatic stability when incorporated in RNA oligonucleotides. As it has been demonstrated that even a single cyclohexenyl nucleoside, when incorporated in an oligonucleotide, can have a profound effect on the biological activity of the oligonucleotide, further research is warranted to study the complex of such oligonucleotides with target proteins. In order to analyse the influence of CeNA residues onto the helix conformation and hydration of natural nucleic acid structures, a cyclohexenyl-adenine building block (xAr) was incorporated into the Dickerson sequence CGCGA(xAr)TTCGCG. The crystal structure of this sequence determined to a resolution of 1.90 A. The global helix belongs to the B-type family and shows a water spine, which is partially broken up by the apolar cyclohexene residue. The cyclohexene ring adopts the (2)E-conformation allowing a better incorporation of the residue in the dodecamer sequence. The crystal packing is stabilized by cobalt hexamine residues and belongs to space group P222(1), never before reported for nucleic acids.
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==About this Structure==
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Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG).,Robeyns K, Herdewijn P, Van Meervelt L Nucleic Acids Res. 2008 Mar;36(5):1407-14. Epub 2007 Dec 26. PMID:18160414<ref>PMID:18160414</ref>
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2P8D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Known structural/functional Sites: <scene name='pdbsite=AC1:Xar+Binding+Site+For+Residue+A+6'>AC1</scene>, <scene name='pdbsite=AC2:Xar+Binding+Site+For+Residue+B+6'>AC2</scene>, <scene name='pdbsite=AC3:Nco+Binding+Site+For+Residue+B+101'>AC3</scene>, <scene name='pdbsite=AC4:Nco+Binding+Site+For+Residue+B+102'>AC4</scene> and <scene name='pdbsite=AC5:Nco+Binding+Site+For+Residue+B+103'>AC5</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2P8D OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Influence of the incorporation of a cyclohexenyl nucleic acid (CeNA) residue onto the sequence d(CGCGAATTCGCG)., Robeyns K, Herdewijn P, Van Meervelt L, Nucleic Acids Res. 2007 Dec 26;. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=18160414 18160414]
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</div>
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[[Category: Single protein]]
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<div class="pdbe-citations 2p8d" style="background-color:#fffaf0;"></div>
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[[Category: Meervelt, L.Van.]]
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== References ==
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[[Category: Robeyns, K.]]
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<references/>
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[[Category: NCO]]
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__TOC__
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[[Category: cena]]
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</StructureSection>
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[[Category: dna]]
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[[Category: Large Structures]]
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[[Category: sugar modification]]
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[[Category: Robeyns K]]
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[[Category: Van Meervelt L]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 6 17:23:12 2008''
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Current revision

The Structure of the Dickerson Sequence with an Incorporated CeNA Residue

PDB ID 2p8d

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