Summary information and primary citation
- PDB-id
-
198d;
SNAP-derived features in text and
JSON formats
- Class
- DNA
- Method
- X-ray (1.97 Å)
- Summary
- A trigonal form of the idarubicin-d(cgatcg) complex:
crystal and molecular structure at 2.0 angstroms
resolution
- Reference
-
Dautant A, Langlois d'Estaintot B, Gallois B, Brown T,
Hunter WN (1995): "A trigonal
form of the idarubicin:d(CGATCG) complex; crystal and
molecular structure at 2.0 A resolution." Nucleic
Acids Res., 23, 1710-1716. doi:
10.1093/nar/23.10.1710.
- Abstract
- The X-ray crystal structure of the complex between the
anthracycline idarubicin and d(CGATCG) has been solved by
molecular replacement and refined to a resolution of 2.0 A.
The final R-factor is 0.19 for 3768 reflections with Fo
> or = 2 sigma (Fo). The complex crystallizes in the
trigonal space group P31 with unit cell parameters a = b =
52.996(4), c = 33.065(2) A, alpha = beta = 90 degree, gamma
= 120 degree. The asymmetric unit consists of two duplexes,
each one being complexed with two idarubicin drugs
intercalated at the CpG steps, one spermine and 160 water
molecules. The molecular packing underlines major
groove-major groove interactions between neighbouring
helices, and an unusually low value of the occupied
fraction of the unit cell due to a large solvent channel of
approximately 30 A diameter. This is the first trigonal
crystal form of a DNA-anthracycline complex. The structure
is compared with the previously reported structure of the
same complex crystallizing in a tetragonal form. The
geometry of both the double helices and the intercalation
site are conserved as are the intramolecular interactions
despite the different crystal forms.
