1D8G
ULTRAHIGH RESOLUTION CRYSTAL STRUCTURE OF B-DNA DECAMER D(CCAGTACTGG)
Summary for 1D8G
| Entry DOI | 10.2210/pdb1d8g/pdb |
| Descriptor | 5'-D(*CP*CP*AP*GP*TP*AP*CP*TP*GP*GP*)-3', CALCIUM ION (3 entities in total) |
| Functional Keywords | b-dna, alternate conformation, ultrahigh resolution, trp repressor, polyamide, dna |
| Total number of polymer chains | 1 |
| Total formula weight | 3205.32 |
| Authors | Kielkopf, C.L.,Ding, S.,Kuhn, P.,Rees, D.C. (deposition date: 1999-10-23, release date: 2000-02-21, Last modification date: 2024-02-07) |
| Primary citation | Kielkopf, C.L.,Ding, S.,Kuhn, P.,Rees, D.C. Conformational flexibility of B-DNA at 0.74 A resolution: d(CCAGTACTGG)(2). J.Mol.Biol., 296:787-801, 2000 Cited by PubMed Abstract: The affinity and specificity of a ligand for its DNA site is a function of the conformational changes between the isolated and complexed states. Although the structures of a hydroxypyrrole-imidazole-pyrrole polyamide dimer with 5'-CCAGTACTGG-3' and the trp repressor recognizing the sequence 5'-GTACT-3' are known, the baseline conformation of the DNA site would contribute to our understanding of DNA recognition by these ligands. The 0.74 A resolution structure of a B-DNA double helix, 5'-CCAGTACTGG-3', has been determined by X-ray crystallography. Six of the nine phosphates, two of four bound calcium ions and networks of water molecules hydrating the oligonucleotide have alternate conformations. By contrast, nine of the ten bases have a single, unique conformation with hydrogen atoms visible in most cases. The polyamide molecules alter the geometry of the phosphodiester backbone, and the water molecules mediating contacts in the trp repressor/operator complex are conserved in the unliganded DNA. Furthermore, the multiple conformational states, ions and hydration revealed by this ultrahigh resolution structure of a B-form oligonucleotide are potentially general considerations for understanding DNA-binding affinity and specificity by ligands. PubMed: 10677281DOI: 10.1006/jmbi.1999.3478 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (0.74 Å) |
Structure validation
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