1DN8

STRUCTURE OF A Z-DNA WITH TWO DIFFERENT BACKBONE CHAIN CONFORMATIONS. STABILIZATION OF THE DECADEOXYOLIGONUCLEOTIDE D(CGTACGTACG) BY (CO(NH3)6)3+ BINDING TO THE GUANINE

Summary for 1DN8

• Entry DOI: 10.2210/pdb1dn8/pdb
• Descriptor: DNA (5'-D(*P*CP*GP*TP*AP*CP*GP*TP*AP*CP*G)-3'), COBALT HEXAMMINE(III) (2 entities in total)
• Functional Keywords: z-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 1338.00

Authors

Brennan, R.G.,Westhof, E.,Sundaralingam, M. (deposition date: 1987-05-12, release date: 1988-04-16, Last modification date: 2024-02-07)

Primary citation

Brennan, R.G.,Westhof, E.,Sundaralingam, M.
Structure of a Z-DNA with two different backbone chain conformations. Stabilization of the decadeoxyoligonucleotide d(CGTACGTACG) by [Co(NH3)6]3+ binding to the guanine.
J.Biomol.Struct.Dyn., 3:649-665, 1986

PubMed Abstract: The complex between cobalt hexammine and decadeoxyoligomer d(CGTACGTACG) crystallizes into the space group P65 with unit cell constants a = b = 17.93A, and c = 43.41A. The molecules have the helix axis coincident with the crystal c-axis. The decamers stack on top of each other and form a quasi-continuous helix. The structure is disordered. The asymmetric unit is a dimer (pPyr-pPur)2 with each base pair 60% of the time a C-G and 40% of the time a T-A. Restrainted least-squares refinement led to an R-factor of 25.5% for 506 observed reflections above the two-sigma level. The structure was found to have one strand in the ZI-conformation and the other in the ZII-conformation. The cobalt hexammine binds to two ZII-chains of symmetrically related molecules. On one ZII chain, two ammonia molecules of the cobalt hexammine bind to the N7 nitrogen and 06 oxygen atoms of the guanine bases and a third ammonia to the phosphate anionic oxygen atom of the preceding pyrimidine base, resulting in an "external" binding mode. On the other ZII chain, one ammonia molecule of the cobalt hexammine binds only to the anionic oxygens of the phosphate group of the guanine bases, leading to an "internal" binding mode. Thus, the basis of the stabilization of Z-DNA by [Co(NH3)6]3+ is its binding to only guanine nucleotides. It is surmised that statistical disordering of deoxyoligonucleotide structures which take a Z conformation, depends on the length of the oligomer. That is to say, octamers and decamers (which cannot use an integral number of molecules for a 12 base pair repeat) form disordered structures whereas tetramers and hexamers form well ordered structures.

PubMed: 3271042

Experimental method

X-RAY DIFFRACTION (1.5 Å)