3CWT: Crystal Structure Of An Alka Host/guest Complex 2'-fluoro-2'- Deoxyinosine:adenine Base Pair

The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.
PDB ID: 3CWTDownload
MMDB ID: 66467
PDB Deposition Date: 2008/4/22
Updated in MMDB: 2017/11
Experimental Method:
x-ray diffraction
Resolution: 2.3  Å
Source Organism:
Escherichia coli
Similar Structures:
Biological Unit for 3CWT: octameric; determined by author and by software (PISA)
Molecular Components in 3CWT
Label Count Molecule
Proteins (4 molecules)
DNA-3-methyladenine Glycosylase 2(Gene symbol: alkA)
Molecule annotation
Nucleotides(2 molecules)
DNA (5'-d(*dgp*dap*dcp*dap*dtp*dgp*dap*(2fi) P*dtp*dgp*dcp*dc)-3')
Molecule annotation
DNA (5'-d(*dgp*dgp*dcp*dap*dap*dtp*dcp*dap*dtp*dgp*dtp*dc)- 3')
Molecule annotation
* Click molecule labels to explore molecular sequence information.

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