1ply: Difference between revisions

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[[Image:1ply.gif|left|200px]]


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==SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)==
The line below this paragraph, containing "STRUCTURE_1ply", creates the "Structure Box" on the page.
<StructureSection load='1ply' size='340' side='right'caption='[[1ply]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
You may change the PDB parameter (which sets the PDB file loaded into the applet)
== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1ply]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PLY FirstGlance]. <br>
or leave the SCENE parameter empty for the default display.
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Fiber diffraction, [[Resolution|Resolution]] 3.2&#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=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1ply|  PDB=1ply  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ply FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ply OCA], [https://pdbe.org/1ply PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ply RCSB], [https://www.ebi.ac.uk/pdbsum/1ply PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ply ProSAT]</span></td></tr>
 
</table>
'''SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Chandrasekaran R]]
Analysis of X-ray diffraction data from a polycrystalline and well oriented fiber of the sodium salt of poly(dA).poly(dT) shows that this B'-DNA corresponds to a right-handed antiparallel tenfold double-helix of pitch 32.4 A, with C2'-endo furanose rings in both strands. The helix contrasts itself from B-DNA in terms of a very narrow minor groove. Difference electron-density maps have revealed that a continuous spine of water molecules, two per base pair, propagates along this groove with the same symmetry as the DNA and establishes new links between the two strands. In addition to this hydrated DNA helix, the monoclinic unit cell (space group P2(1)) accommodates about 20 sodium ions and 12 water molecules in the vicinity of phosphate groups. These structured guest molecules provide an intricate network of bridges, ranging in size from a single sodium ion to a multiple sodium-water-water-sodium unit, connecting phosphate groups belonging to adjacent DNA helices. The crystallographic R value for this structure is 0.23 for a total of 102 reflections extending out to 3.2 A resolution.
[[Category: Park H-S]]
 
[[Category: Radha A]]
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PLY OCA].  
 
==Reference==
Sodium ions and water molecules in the structure of poly(dA).poly(dT)., Chandrasekaran R, Radha A, Park HS, Acta Crystallogr D Biol Crystallogr. 1995 Nov 1;51(Pt 6):1025-35. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15299771 15299771]
[[Category: Chandrasekaran, R.]]
[[Category: Park, H S.]]
[[Category: Radha, A.]]
[[Category: Dna]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 05:14:10 2008''

Latest revision as of 11:09, 14 February 2024

SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)SODIUM IONS AND WATER MOLECULES IN THE STRUCTURE OF POLY D(A)(DOT)POLY D(T)

Structural highlights

1ply is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Fiber diffraction, Resolution 3.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1ply, resolution 3.20Å

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