1dnx: Difference between revisions
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=" | [[Image:1dnx.gif|left|200px]]<br /><applet load="1dnx" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1dnx, resolution 1.70Å" /> | caption="1dnx, resolution 1.70Å" /> | ||
'''RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES'''<br /> | '''RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES'''<br /> | ||
==Overview== | ==Overview== | ||
Magnesium ions play important roles in the structure and function of | 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. | ||
==About this Structure== | ==About this Structure== | ||
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:// | 1DNX is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNX OCA]. | ||
==Reference== | ==Reference== | ||
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] | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Gao, Y | [[Category: Gao, Y G.]] | ||
[[Category: Joachimiak, A.]] | [[Category: Joachimiak, A.]] | ||
[[Category: Robinson, H.]] | [[Category: Robinson, H.]] | ||
[[Category: Sanishvili, R.]] | [[Category: Sanishvili, R.]] | ||
[[Category: Wang, A | [[Category: Wang, A H.J.]] | ||
[[Category: MG]] | [[Category: MG]] | ||
[[Category: dna conformation]] | [[Category: dna conformation]] | ||
| Line 22: | Line 22: | ||
[[Category: rna/dna hybrid]] | [[Category: rna/dna hybrid]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:18:33 2008'' | ||
Revision as of 13:18, 21 February 2008
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RNA/DNA DODECAMER R(G)D(CGTATACGC) WITH MAGNESIUM BINDING SITES
OverviewOverview
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.
About this StructureAbout this Structure
1DNX is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
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
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