8A71
Crystal structure of right-handed Z-DNA containing 2'-deoxy-L-ribose in complex with the polyamine cadaverine and potassium cations at ultrahigh resolution
Summary for 8A71
| Entry DOI | 10.2210/pdb8a71/pdb |
| Related | 4hif 4hig 4r15 5jzq 7atg |
| Descriptor | Right-handed Z-DNA, 5-azaniumylpentylazanium, POTASSIUM ION, ... (4 entities in total) |
| Functional Keywords | z-dna, dna, right-handed z-dna, cadaverine, potassium, cadaverinium cation, biogenic polyamines, 2-deoxy-l-ribose |
| Biological source | synthetic construct |
| Total number of polymer chains | 2 |
| Total formula weight | 3763.70 |
| Authors | Drozdzal, P.,Manszewski, T.,Gilski, M.,Brzezinski, K.,Jaskolski, M. (deposition date: 2022-06-20, release date: 2023-02-22, Last modification date: 2024-02-07) |
| Primary citation | Drozdzal, P.,Manszewski, T.,Gilski, M.,Brzezinski, K.,Jaskolski, M. Right-handed Z-DNA at ultrahigh resolution: a tale of two hands and the power of the crystallographic method. Acta Crystallogr D Struct Biol, 79:133-139, 2023 Cited by PubMed Abstract: The self-complementary L-d(CGCGCG) purine/pyrimidine hexanucleotide was crystallized in complex with the polyamine cadaverine and potassium cations. Since the oligonucleotide contained the enantiomeric 2'-deoxy-L-ribose, the Z-DNA duplex is right-handed, as confirmed by the ultrahigh-resolution crystal structure determined at 0.69 Å resolution. Although the X-ray diffraction data were collected at a very short wavelength (0.7085 Å), where the anomalous signal of the P and K atoms is very weak, the signal was sufficiently outstanding to clearly indicate the wrong hand when the structure was mistakenly solved assuming the presence of 2'-deoxy-D-ribose. The electron density clearly shows the entire cadaverinium dication, which has an occupancy of 0.53 and interacts with one Z-DNA duplex. The K cation, with an occupancy of 0.32, has an irregular coordination sphere that is formed by three OP atoms of two symmetry-related Z-DNA duplexes and one O5' hydroxyl O atom, and is completed by three water sites, one of which is twofold disordered. The K site is complemented by a partial water molecule, the hydrogen bonds of which have the same lengths as the K-O bonds. The sugar-phosphate backbone assumes two conformations, but the base pairs do not show any sign of disorder. PubMed: 36762859DOI: 10.1107/S2059798322011937 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (0.69 Å) |
Structure validation
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