1l6b: Difference between revisions
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|PDB= 1l6b |SIZE=350|CAPTION= <scene name='initialview01'>1l6b</scene>, resolution 1.5Å | |PDB= 1l6b |SIZE=350|CAPTION= <scene name='initialview01'>1l6b</scene>, resolution 1.5Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=CA:CALCIUM ION'>CA</scene> | |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1l6b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l6b OCA], [http://www.ebi.ac.uk/pdbsum/1l6b PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1l6b RCSB]</span> | |||
}} | }} | ||
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[[Category: Ho, P S.]] | [[Category: Ho, P S.]] | ||
[[Category: Vargason, J M.]] | [[Category: Vargason, J M.]] | ||
[[Category: cytosine methylation]] | [[Category: cytosine methylation]] | ||
[[Category: dna four-way junction]] | [[Category: dna four-way junction]] | ||
[[Category: holliday junction]] | [[Category: holliday junction]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:58:40 2008'' | ||
Revision as of 21:58, 30 March 2008
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| , resolution 1.5Å | |||||||
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| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE ANALYSIS OF THE ALL DNA HOLLIDAY JUNCTION STRUCTURE OF CCGGTACM5CGG
OverviewOverview
The single crystal structure of the methylated sequence d(CCGGTACm(5)CGG) has been solved as an antiparallel stacked X Holliday junction to 1.5 A resolution. When compared with the parent nonmethylated d(CCGGTACCGG) structure, the duplexes are translated by 3.4 A along the helix axis and rotated by 10.8 degrees relative to each other, rendering the major grooves more accessible overall. A Ca(2+) complex is seen in the minor groove opposite the junction but is related to the B conformation of the stacked arms. At the junction itself, the hydrogen bond from the N4 nitrogen of cytosine C8 to the C7 phosphate at the crossover in the parent structure has been replaced by a water bridge. Thus, this direct interaction is not absolutely required to stabilize the junction at the previously defined ACC trinucleotide core. The more compact methylated junction forces the Na(+) of the protected central cavity of the nonmethylated junction into a solvent cluster that spans the space between the junction crossover and the stacked arms. A series of void volumes within the methylated and the nonmethylated structures suggests that small monovalent cations can fill and vacate this central cavity without the need to unfold the four-stranded Holliday junction completely.
About this StructureAbout this Structure
1L6B is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution., Vargason JM, Ho PS, J Biol Chem. 2002 Jun 7;277(23):21041-9. Epub 2002 Mar 27. PMID:11919197
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