1XA2

Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA).d(TGCGCG) in two crystal forms

Summary for 1XA2

• Entry DOI: 10.2210/pdb1xa2/pdb
• Descriptor: 5'-D(*CP*GP*CP*GP*CP*A)-3', 5'-D(*TP*GP*CP*GP*CP*G)-3', COBALT HEXAMMINE(III), ... (4 entities in total)
• Functional Keywords: double helix, z-dna, dna
• Total number of polymer chains: 2
• Total formula weight: 3780.54

Authors

Thiyagarajan, S.,Rajan, S.S.,Gautham, N. (deposition date: 2004-08-25, release date: 2004-11-16, Last modification date: 2024-04-03)

Primary citation

Thiyagarajan, S.,Rajan, S.S.,Gautham, N.
Cobalt hexammine induced tautomeric shift in Z-DNA: the structure of d(CGCGCA)*d(TGCGCG) in two crystal forms.
Nucleic Acids Res., 32:5945-5953, 2004

PubMed Abstract: We report here the crystal structure of the DNA hexamer duplex d(CGCGCA)*d(TGCGCG) at 1.71 A resolution. The crystals, in orthorhombic space group, were grown in the presence of cobalt hexammine, a known inducer of the left-handed Z form of DNA. The interaction of this ion with the DNA helix results in a change of the adenine base from the common amino tautomeric form to the imino tautomer. Consequently the A:T base pair is disrupted from the normal Watson-Crick base pairing to a 'wobble' like base pairing. This change is accommodated easily within the helix, and the helical parameters are those expected for Z-DNA. When the cobalt hexammine concentration is decreased slightly in the crystallization conditions, the duplex crystallizes in a different, hexagonal space group, with two hexamer duplexes in the asymmetric unit. One of these is situated on a crystallographic 6-fold screw axis, leading to disorder. The tautomeric shift is not observed in this space group. We show that the change in inter-helix interactions that lead to the two different space groups probably arise from the small decrease in ion concentration, and consequently disordered positions for the ion.

PubMed: 15534365
DOI: 10.1093/nar/gkh919

Experimental method

X-RAY DIFFRACTION (1.71 Å)