1VT5

THE CRYSTAL STRUCTURE OF D(CCCCGGGG): A NEW A-FORM VARIANT WITH AN EXTENDED BACKBONE CONFORMATION

Summary for 1VT5

• Entry DOI: 10.2210/pdb1vt5/pdb
• Descriptor: DNA (5'-D(*CP*CP*CP*CP*GP*GP*GP*G)-3') (1 entity in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 2428.59

Authors

Haran, T.E.,Shakked, Z.,Wang, A.H.-J.,Rich, A. (deposition date: 1988-08-18, release date: 2011-07-13, Last modification date: 2023-12-27)

Primary citation

Haran, T.E.,Shakked, Z.,Wang, A.H.,Rich, A.
The crystal structure of d(CCCCGGGG): a new A-form variant with an extended backbone conformation.
J.Biomol.Struct.Dyn., 5:199-217, 1987

PubMed Abstract: The crystal structure of d(CCCCGGGG) has been determined at a resolution of 2.25 A. The oligomers crystallize as A-DNA duplexes occupying crystallographic two-fold axes. The backbone conformation is, in general, similar to that observed in previously reported crystal structures of A-DNA fragments, except for the central linkage, where it adopts an extended structure resulting from all trans conformation at the P-O5'-C5'-C4' bonds. This type of conformation facilitates interstrand stacking between the guanines at the C-G site. The local helix twist at this step is very small (25 degrees) compared to an overall average of 33.5 degrees. The unique structure of the C-G base-pair step, namely the extended backbone and the distinct stacking geometry, may be an important feature in the recognition mechanism between double-stranded DNA molecules and restriction endonucleases such as Msp I, which cuts the sequence CCGG very specifically with a rate unaffected by neighboring base pairs.

PubMed: 3271472

Experimental method

X-RAY DIFFRACTION (2.25 Å)