This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

220d

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/220d"

Categories: Large Structures | Gao Y-G | Robinson H | Van Boom JH | Wang AH-J

@@ Line 1: / Line 1: @@
-[[Image:220d.jpg|left|200px]]<br /><applet load="220d" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="220d, resolution 2.000&Aring;" />
-'''INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA'''<br />
-==Overview==
+==INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA==
-A-DNA is a stable alternative right-handed double helix that is favored by, certain sequences (e.g., (dG)n.(dC)n) or under low humidity conditions., Earlier A-DNA structures of several DNA oligonucleotides and RNA.DNA, chimeras have revealed some conformational variation that may be the, result of sequence-dependent effects or crystal packing forces. In this, study, four crystal structures of three decamer oligonucleotides, d(ACCGGCCGGT), d(ACCCGCGGGT), and r(GC)d(GTATACGC) in two crystal forms, (either the P6(1)22 or the P2(1)2(1)2(1) space group) have been analyzed, at high resolution to provide the molecular basis of the structural, difference in an experimentally consistent manner. The study reveals that, molecules crystallized in the same space group have a more similar A-DNA, conformation, whereas the same molecule crystallized in different space, groups has different (local) conformations. This suggests that even though, the local structure is influenced by the crystal packing environments, the, DNA molecule adjusts to adopt an overall conformation close to canonical, A-DNA. For example, the six independent CpG steps in these four structures, have different base-base stacking patterns, with their helical twist, angles (omega) ranging from 28 degrees to 37 degrees. Our study further, reveals the structural impact of different counter-ions on the A-DNA, conformers. [Co(NH3)6]3+ has three unique A-DNA binding modes. One binds, at the major groove side of a GpG step at the O6/N7 sites of guanine bases, via hydrogen bonds. The other two modes involve the binding of ions to, phosphates, either bridging across the narrow major groove or binding, between two intra-strand adjacent phosphates. Those interactions may, explain the recent spectroscopic and NMR observations that [Co(NH3)6]3+ is, effective in inducing the B- to A-DNA transition for DNA with (G)n, sequence. Interestingly, Ba2+ binds to the same O6/N7 sites on guanine by, direct coordinations.
+<StructureSection load='220d' size='340' side='right'caption='[[220d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[220d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=220D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=220D FirstGlance]. <br>
-D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=BA:'>BA</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=220D 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]] 2&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BA:BARIUM+ION'>BA</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=220d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=220d OCA], [https://pdbe.org/220d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=220d RCSB], [https://www.ebi.ac.uk/pdbsum/220d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=220d ProSAT]</span></td></tr>
-Influence of counter-ions on the crystal structures of DNA decamers: binding of [Co(NH3)6]3+ and Ba2+ to A-DNA., Gao YG, Robinson H, van Boom JH, Wang AH, Biophys J. 1995 Aug;69(2):559-68. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8527670 8527670]
+</table>
-[[Category: Protein complex]]
+__TOC__
-[[Category: Boom, J.H.Van.]]
+</StructureSection>
-[[Category: Gao, Y.G.]]
+[[Category: Large Structures]]
-[[Category: Robinson, H.]]
+[[Category: Gao Y-G]]
-[[Category: Wang, A.H.J.]]
+[[Category: Robinson H]]
-[[Category: BA]]
+[[Category: Van Boom JH]]
-[[Category: a-dna]]
+[[Category: Wang AH-J]]
-[[Category: double helix]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri Feb 15 17:13:48 2008''

220d

From Proteopedia

Current revision

INFLUENCE OF COUNTER-IONS ON THE CRYSTAL STRUCTURES OF DNA DECAMERS: BINDING OF [CO(NH3)6]3+ AND BA2+ TO A-DNA

Structural highlights

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox