1s1l: Difference between revisions

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[[Image:1s1l.gif|left|200px]]


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==Influence of Groove Interactions on the Formation of DNA Holliday Junctions==
The line below this paragraph, containing "STRUCTURE_1s1l", creates the "Structure Box" on the page.
<StructureSection load='1s1l' size='340' side='right'caption='[[1s1l]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
<table><tr><td colspan='2'>[[1s1l]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1S1L 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]] 2.2&#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=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene></td></tr>
{{STRUCTURE_1s1l|  PDB=1s1l  |  SCENE= }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1s1l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1s1l OCA], [https://pdbe.org/1s1l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1s1l RCSB], [https://www.ebi.ac.uk/pdbsum/1s1l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1s1l ProSAT]</span></td></tr>
 
</table>
'''Influence of Groove Interactions on the Formation of DNA Holliday Junctions'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Hays FA]]
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.
[[Category: Ho PS]]
 
[[Category: Jones ZJ]]
==About this Structure==
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1S1L OCA].  
 
==Reference==
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: Jones, Z J.]]
[[Category: Dna four-way junction]]
[[Category: Holliday junction]]
[[Category: Inosine]]
[[Category: Major groove]]
[[Category: Minor groove]]
[[Category: X-ray diffraction]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 08:10:57 2008''

Latest revision as of 11:27, 14 February 2024

Influence of Groove Interactions on the Formation of DNA Holliday JunctionsInfluence of Groove Interactions on the Formation of DNA Holliday Junctions

Structural highlights

1s1l is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1s1l, resolution 2.20Å

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