1dnx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
m (Protected "1dnx" [edit=sysop:move=sysop])
Current revision (06:56, 7 February 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
 +
==RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES==
==RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES==
-
<StructureSection load='1dnx' size='340' side='right' caption='[[1dnx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
+
<StructureSection load='1dnx' size='340' side='right'caption='[[1dnx]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DNX FirstGlance]. <br>
+
<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>
-
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene><br>
+
</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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dno|1dno]], [[1dnt|1dnt]]</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>
-
<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dnx RCSB], [http://www.ebi.ac.uk/pdbsum/1dnx PDBsum]</span></td></tr>
+
<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>
-
<table>
+
</table>
-
<div style="background-color:#fffaf0;">
+
-
== Publication Abstract from PubMed ==
+
-
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.
+
-
 
+
-
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:10734195<ref>PMID:10734195</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Gao, Y G.]]
+
[[Category: Large Structures]]
-
[[Category: Joachimiak, A.]]
+
[[Category: Gao Y-G]]
-
[[Category: Robinson, H.]]
+
[[Category: Joachimiak A]]
-
[[Category: Sanishvili, R.]]
+
[[Category: Robinson H]]
-
[[Category: Wang, A H.J.]]
+
[[Category: Sanishvili R]]
-
[[Category: Dna conformation]]
+
[[Category: Wang AH-J]]
-
[[Category: Dna-rna complex]]
+
-
[[Category: Dna-rna hybrid]]
+
-
[[Category: Metal ion]]
+
-
[[Category: Rna/dna hybrid]]
+

Current revision

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

PDB ID 1dnx

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1dnx"
Personal tools