3u08 | pdb_00003u08

Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution

spinqualitylabelsall models 3u08, resolution 1.25Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3u08 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: D63, MG Related: 3u05 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed High-resolution crystal structures of the DNA duplex sequence d(CGCGAATTCGCG)(2) complexed with three minor-groove ligands are reported. A highly conserved cluster of 11 linked water molecules has been found in the native and all 3 ligand-bound structures, positioned at the boundary of the A/T and G/C regions where the minor groove widens. This cluster appears to play a key structural role in stabilizing noncovalently binding small molecules in the AT region of the B-DNA minor groove. The cluster extends from the backbone phosphate groups along the mouth of the groove and links to DNA and ligands by a network of hydrogen bonds that help to maintain the ligands in position. This arrangement of water molecules is distinct from, but linked by, hydrogen bonding to the well-established spine of hydration, which is displaced by bound ligands. Features of the water cluster and observed differences in binding modes help to explain the measured binding affinities and thermodynamic characteristics of these ligands on binding to AT sites in DNA. Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.,Wei D, Wilson WD, Neidle S J Am Chem Soc. 2013 Jan 30;135(4):1369-77. doi: 10.1021/ja308952y. Epub 2013 Jan , 16. PMID:23276263 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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