232D
THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)
Summary for 232D
| Entry DOI | 10.2210/pdb232d/pdb |
| Descriptor | DNA (5'-D(*AP*GP*GP*CP*AP*TP*GP*CP*CP*T)-3'), COBALT HEXAMMINE(III) (3 entities in total) |
| Functional Keywords | a-dna, double helix, flipped-out bases, dna |
| Total number of polymer chains | 1 |
| Total formula weight | 3367.24 |
| Authors | Nunn, C.M.,Neidle, S. (deposition date: 1995-09-05, release date: 1996-03-22, Last modification date: 2024-02-14) |
| Primary citation | Nunn, C.M.,Neidle, S. The high resolution crystal structure of the DNA decamer d(AGGCATGCCT). J.Mol.Biol., 256:340-351, 1996 Cited by PubMed Abstract: The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symmetry-related strands. The central eight bases of the decamer form an A-DNA octamer duplex with one symmetry-related strand whilst the terminal 5'-A and T-3' bases are flipped out and away from the octamer helix axis to form base-pairing interactions with a second symmetry-related strand. These A.T base-pairs lie perpendicular to the crystallographic c axis and pack within the unit cell in conjunction with a symmetry-related A.T base-pair displaced by 3.4 A degrees along the c axis. A novel base triplet interaction of the type A*(G.C) is present in the structure with interaction from the major groove side of the terminal 5'-A base to the minor groove of the central A-DNA octamer. This structure reports the first example of cobalt hexammine binding to a right-handed DNA duplex. The crystallographic asymmetric unit contains two cobalt hexammine ligands with one site in the major groove coordinating via hydrogen bonds to the 5'-AGG bases, and the second site located between DNA molecules and interacting with the oxygen atoms of phosphate groups. PubMed: 8594201DOI: 10.1006/jmbi.1996.0090 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.3 Å) |
Structure validation
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