1dnx: Difference between revisions

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New page: left|200px<br /><applet load="1dnx" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dnx, resolution 1.70Å" /> '''RNA/DNA DODECAMER R(...
 
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[[Image:1dnx.gif|left|200px]]<br /><applet load="1dnx" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1dnx, resolution 1.70&Aring;" />
'''RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES'''<br />


==Overview==
==RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES==
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.
<StructureSection load='1dnx' size='340' side='right'caption='[[1dnx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
 
== Structural highlights ==
==About this Structure==
<table><tr><td colspan='2'>[[1dnx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNX FirstGlance]. <br>
1DNX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DNX OCA].  
</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>
 
<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>
==Reference==
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1dnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnx OCA], [https://pdbe.org/1dnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnx RCSB], [https://www.ebi.ac.uk/pdbsum/1dnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnx ProSAT]</span></td></tr>
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=10734195 10734195]
</table>
[[Category: Protein complex]]
__TOC__
[[Category: Gao, Y.G.]]
</StructureSection>
[[Category: Joachimiak, A.]]
[[Category: Large Structures]]
[[Category: Robinson, H.]]
[[Category: Gao Y-G]]
[[Category: Sanishvili, R.]]
[[Category: Joachimiak A]]
[[Category: Wang, A.H.J.]]
[[Category: Robinson H]]
[[Category: MG]]
[[Category: Sanishvili R]]
[[Category: dna conformation]]
[[Category: Wang AH-J]]
[[Category: metal ions]]
[[Category: rna/dna hybrid]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 03:25:22 2007''

Latest revision as of 09:56, 7 February 2024

RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITESRNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES

Structural highlights

1dnx is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1dnx, resolution 1.70Å

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