1UHX

Crystal structure of d(GCGAGAGC): the base-intercalated duplex

Summary for 1UHX

• Entry DOI: 10.2210/pdb1uhx/pdb
• Related: 1UHY
• Descriptor: 5'-D(*GP*(CBR)P*GP*AP*GP*AP*GP*C)-3', MAGNESIUM ION, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: base-intercalated duplex, base-intercalated motif, sheared g:a pair, dna, deoxyribonucleic acid
• Total number of polymer chains: 1
• Total formula weight: 2799.40

Authors

Kondo, J.,Umeda, S.I.,Fujita, K.,Sunami, T.,Takenaka, A. (deposition date: 2003-07-13, release date: 2004-02-03, Last modification date: 2023-12-27)

Primary citation

Kondo, J.,Umeda, S.I.,Fujita, K.,Sunami, T.,Takenaka, A.
X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.
J.Synchrotron Radiat., 11:117-120, 2004

PubMed Abstract: DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.

PubMed: 14646150
DOI: 10.1107/S0909049503023562

Experimental method

X-RAY DIFFRACTION (2 Å)