2fij

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[[Image:2fij.gif|left|200px]]
 
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==Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)==
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The line below this paragraph, containing "STRUCTURE_2fij", creates the "Structure Box" on the page.
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<StructureSection load='2fij' size='340' side='right'caption='[[2fij]], [[Resolution|resolution]] 1.19&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2fij]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FIJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2FIJ 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]] 1.19&#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=A2M:2-O-METHYLADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>A2M</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene>, <scene name='pdbligand=UAR:URACIL+ARABINOSE-5-PHOSPHATE'>UAR</scene></td></tr>
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{{STRUCTURE_2fij| PDB=2fij | SCENE= }}
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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=2fij FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2fij OCA], [https://pdbe.org/2fij PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2fij RCSB], [https://www.ebi.ac.uk/pdbsum/2fij PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2fij ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.
2'-Deoxy-2'-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A- and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A- and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.
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==About this Structure==
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2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H.,Li F, Sarkhel S, Wilds CJ, Wawrzak Z, Prakash TP, Manoharan M, Egli M Biochemistry. 2006 Apr 4;45(13):4141-52. PMID:16566588<ref>PMID:16566588</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2FIJ 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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2'-Fluoroarabino- and arabinonucleic acid show different conformations, resulting in deviating RNA affinities and processing of their heteroduplexes with RNA by RNase H., Li F, Sarkhel S, Wilds CJ, Wawrzak Z, Prakash TP, Manoharan M, Egli M, Biochemistry. 2006 Apr 4;45(13):4141-52. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16566588 16566588]
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</div>
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[[Category: Egli, M.]]
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<div class="pdbe-citations 2fij" style="background-color:#fffaf0;"></div>
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[[Category: Li, F.]]
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== References ==
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[[Category: A-form dna]]
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<references/>
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[[Category: Arabinonucleic acid]]
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__TOC__
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[[Category: Sugar modification]]
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</StructureSection>
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 03:56:20 2008''
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[[Category: Large Structures]]
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[[Category: Egli M]]
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[[Category: Li F]]

Current revision

Crystal Structure Analysis of the A-DNA Decamer GCGT-2'OMeA-aU-ACGC, with Incorporated 2'-O-Methylated-Adenosine (2'OMeA) and Arabino-Uridine (aU)

PDB ID 2fij

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