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2hpx
From Proteopedia
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| - | [[Image:2hpx.gif|left|200px]] | + | [[Image:2hpx.gif|left|200px]] |
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| - | '''13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure''' | + | {{Structure |
| + | |PDB= 2hpx |SIZE=350|CAPTION= <scene name='initialview01'>2hpx</scene> | ||
| + | |SITE= | ||
| + | |LIGAND= | ||
| + | |ACTIVITY= | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2HPX is a [ | + | 2HPX is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HPX OCA]. |
==Reference== | ==Reference== | ||
| - | Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites., Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J, Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:[http:// | + | Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites., Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J, Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17323932 17323932] |
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Case, D A.]] | [[Category: Case, D A.]] | ||
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[[Category: bleomycin]] | [[Category: bleomycin]] | ||
[[Category: dna damage]] | [[Category: dna damage]] | ||
| - | [[Category: molecular | + | [[Category: molecular dynamic]] |
[[Category: nmr]] | [[Category: nmr]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:20:04 2008'' |
Revision as of 15:20, 20 March 2008
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| Coordinates: | save as pdb, mmCIF, xml | ||||||
13mer Duplex DNA containing a 4'-oxidized abasic site, averaged structure
Overview
A 4'-oxidized abasic site (X) has been synthesized in a defined duplex DNA sequence, 5'-d(CCAAAGXACCGGG)-3'/3'-d(GGTTTCATGGCCC)-5' (1). Its structure has been determined by two-dimensional NMR methods, molecular modeling, and molecular dynamics simulations. 1 is globally B-form with the base (A) opposite X intrahelical and well-stacked. Only the alpha anomer of X is observed, and the abasic site deoxyribose is largely intrahelical. These results are compared with a normal abasic site (Y) in the same sequence context (2). Y is composed of a 60:40 mixture of alpha and beta anomers (2alpha and 2beta). In both 2alpha and 2beta, the base (A) opposite Y is intrahelical and well-stacked and the abasic site deoxyribose is predominantly extrahelical, consistent with the reported structures of the normal abasic site in a similar sequence context [Hoehn, S. T., Turner, C. J., and Stubbe, J. (2001) Nucleic Acids Res. 29, 3413-3423]. Molecular dynamics simulations reveal that the normal abasic site appears to be conformationally more flexible than the 4'-oxidized abasic site. The importance of the structure and flexibility of the abasic site in the recognition by the DNA repair enzyme Ape1 is discussed.
About this Structure
2HPX is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Nuclear magnetic resonance structural studies and molecular modeling of duplex DNA containing normal and 4'-oxidized abasic sites., Chen J, Dupradeau FY, Case DA, Turner CJ, Stubbe J, Biochemistry. 2007 Mar 20;46(11):3096-107. Epub 2007 Feb 27. PMID:17323932
Page seeded by OCA on Thu Mar 20 17:20:04 2008
