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.


431d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:38, 1 March 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:431d.gif|left|200px]]<br /><applet load="431d" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="431d, resolution 1.15&Aring;" />
 
-
'''5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3''''<br />
 
-
==Overview==
+
==5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'==
-
Despite the importance of hydration around DNA in the understanding of its conformation and interactions with other molecules in many biological processes, only limited atomic resolution information is available. Crystal-engineering techniques, which were originally developed to mimic DNA base triplets in a crystal lattice, also eliminate the rotational disorder of oligonucleotides around their helical axis and thereby enhance the resolution of the structure analysis. We have determined the low-temperature crystal structure of the synthetic DNA decamer d(GGCCAATTGG) at atomic resolution (1. 15 A) using 17700 reflections and have characterized the highly organized hydration patterns in both grooves. The narrow d(AATT) minor groove is occupied by an 'extended hydration spine' alternately bridging base pairs and phosphate O1P atoms of opposite strands, while a distinctive pattern of parallel water ribbons is observed in the major groove. This analysis provides structural insight into the correlation found between narrow minor-groove width and occurrence of the B(I) conformation and can be used to design new minor-groove binders. By their location between adjacent helices, two fully hydrated magnesium ions further stabilize the crystal packing. The structure also provides details of the hydration and conformation of G.GC triple helices.
+
<StructureSection load='431d' size='340' side='right'caption='[[431d]], [[Resolution|resolution]] 1.15&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[431d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=431D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=431D FirstGlance]. <br>
-
431D 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=431D 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]] 1.15&#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=431d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=431d OCA], [https://pdbe.org/431d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=431d RCSB], [https://www.ebi.ac.uk/pdbsum/431d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=431d ProSAT]</span></td></tr>
-
B-DNA at atomic resolution reveals extended hydration patterns., Vlieghe D, Turkenburg JP, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 1999 Sep;55(Pt 9):1495-502. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10489444 10489444]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Meervelt, L Van.]]
+
</StructureSection>
-
[[Category: Turkenburg, J P.]]
+
[[Category: Large Structures]]
-
[[Category: Vlieghe, D.]]
+
[[Category: Turkenburg JP]]
-
[[Category: MG]]
+
[[Category: Van Meervelt L]]
-
[[Category: atomic resolution]]
+
[[Category: Vlieghe D]]
-
[[Category: deoxyribonucleic acid]]
+
-
[[Category: double backbone conformation]]
+
-
[[Category: extended hydration spine]]
+
-
[[Category: triplet formation]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:12:07 2008''
+

Current revision

5'-D(*GP*GP*CP*CP*AP*AP*TP*TP*GP*G)-3'

PDB ID 431d

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/431d"
Personal tools