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1dnt

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[[Image:1dnt.gif|left|200px]]
 
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==RNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES==
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The line below this paragraph, containing "STRUCTURE_1dnt", creates the "Structure Box" on the page.
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<StructureSection load='1dnt' size='340' side='right'caption='[[1dnt]], [[Resolution|resolution]] 1.70&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'>[[1dnt]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNT 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]] 1.7&#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=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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{{STRUCTURE_1dnt| PDB=1dnt | 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=1dnt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnt OCA], [https://pdbe.org/1dnt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnt RCSB], [https://www.ebi.ac.uk/pdbsum/1dnt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnt ProSAT]</span></td></tr>
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</table>
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'''RNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES'''
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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==Overview==
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[[Category: Gao Y-G]]
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Magnesium ions play important roles in the structure and function of nucleic acids. Whereas the tertiary folding of RNA often requires magnesium ions binding to tight places where phosphates are clustered, the molecular basis of the interactions of magnesium ions with RNA helical regions is less well understood. We have refined the crystal structures of four decamer oligonucleotides, d(ACCGGCCGGT), r(GCG)d(TATACGC), r(GC)d(GTATACGC) and r(G)d(GCGTATACGC) with bound hexahydrated magnesium ions at high resolution. The structures reveal that A-form nucleic acid has characteristic [Mg(H(2)O)(6)](2+)binding modes. One mode has the ion binding in the deep major groove of a GpN step at the O6/N7 sites of guanine bases via hydrogen bonds. Our crystallographic observations are consistent with the recent NMR observations that in solution [Co(NH(3))(6)](3+), a model ion of [Mg(H(2)O)(6)](2+), binds in an identical manner. The other mode involves the binding of the ion to phosphates, bridging across the outer mouth of the narrow major groove. These [Mg(H(2)O)(6)](2+)ions are found at the most negative electrostatic potential regions of A-form duplexes. We propose that these two binding modes are important in the global charge neutralization, and therefore stability, of A-form duplexes.
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[[Category: Joachimiak A]]
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[[Category: Robinson H]]
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==About this Structure==
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[[Category: Sanishvili R]]
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNT OCA].
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[[Category: Wang AH-J]]
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==Reference==
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Hexahydrated magnesium ions bind in the deep major groove and at the outer mouth of A-form nucleic acid duplexes., Robinson H, Gao YG, Sanishvili R, Joachimiak A, Wang AH, Nucleic Acids Res. 2000 Apr 15;28(8):1760-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10734195 10734195]
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[[Category: Gao, Y G.]]
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[[Category: Joachimiak, A.]]
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[[Category: Robinson, H.]]
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[[Category: Sanishvili, R.]]
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[[Category: Wang, A H.J.]]
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[[Category: Dna conformation]]
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[[Category: Metal ion]]
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[[Category: Rna/dna hybrid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 14:03:40 2008''
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Current revision

RNA/DNA DODECAMER R(GC)D(GTATACGC) WITH MAGNESIUM BINDING SITES

PDB ID 1dnt

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