1s1k: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,615 edits
No edit summary
 
(8 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:1s1k.png|left|200px]]


<!--
==INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION==
The line below this paragraph, containing "STRUCTURE_1s1k", creates the "Structure Box" on the page.
<StructureSection load='1s1k' size='340' side='right'caption='[[1s1k]], [[Resolution|resolution]] 1.90&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'>[[1s1k]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S1K 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">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-->
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1AP:2,6-DIAMINOPURINE+NUCLEOTIDE'>1AP</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
{{STRUCTURE_1s1k|  PDB=1s1k  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s1k FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s1k OCA], [https://pdbe.org/1s1k PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s1k RCSB], [https://www.ebi.ac.uk/pdbsum/1s1k PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s1k ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The inosine-containing sequence d(CCIGTACm(5)CGG) is shown to crystallize as a four-stranded DNA junction. This structure is nearly identical to the antiparallel junction formed by the parent d(CCGGTACm(5)()CGG) sequence [Vargason, J. M., and Ho, P. S. (2002) J. Biol. Chem. 277, 21041-21049] in terms of its conformational geometry, and inter- and intramolecular interactions within the DNA and between the DNA and solvent, even though the 2-amino group in the minor groove of the important G(3).m(5)C(8) base pair of the junction core trinucleotide (italicized) has been removed. In contrast, the analogous 2,6-diaminopurine sequence d(CCDGTACTGG) crystallizes as resolved duplex DNAs, just like its parent sequence d(CCAGTACTGG) [Hays, F. A., Vargason, J. M., and Ho, P. S. (2003) Biochemistry 42, 9586-9597]. These results demonstrate that it is not the presence or absence of the 2-amino group in the minor groove of the R(3).Y(8) base pair that specifies whether a sequence forms a junction, but the positions of the extracyclic amino and keto groups in the major groove. Finally, the study shows that the arms of the junction can accommodate perturbations to the B-DNA conformation of the stacked duplex arms associated with the loss of the 2-amino substituent, and that two hydrogen bonding interactions from the C(7) and Y(8) pyrimidine nucleotides to phosphate oxygens of the junction crossover specify the geometry of the Holliday junction.


===INFLUENCE OF GROOVE INTERACTIONS ON DNA HOLLIDAY JUNCTION FORMATION===
Influence of minor groove substituents on the structure of DNA Holliday junctions.,Hays FA, Jones ZJ, Ho PS Biochemistry. 2004 Aug 3;43(30):9813-22. PMID:15274635<ref>PMID:15274635</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
<!--
</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15274635}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1s1k" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15274635 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15274635}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1K OCA].
[[Category: Hays FA]]
 
[[Category: Ho PS]]
==Reference==
[[Category: Watson J]]
Influence of minor groove substituents on the structure of DNA Holliday junctions., Hays FA, Jones ZJ, Ho PS, Biochemistry. 2004 Aug 3;43(30):9813-22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15274635 15274635]
[[Category: Hays, F A.]]
[[Category: Ho, P S.]]
[[Category: Watson, J.]]
[[Category: 2,6-diaminopurine]]
[[Category: B-dna]]
[[Category: Double helix]]
[[Category: Minor groove interaction]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 05:23:37 2008''
Retrieved from "https://proteopedia.org/1s1k"