3U05

Crystal structure of DB1804-D(CGCGAATTCGCG)2 complex

Summary for 3U05

• Entry DOI: 10.2210/pdb3u05/pdb
• Related: 3U08
• Descriptor: 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', MAGNESIUM ION, 6-(1,4,5,6-tetrahydropyrimidin-2-yl)-2-[4'-(1,4,5,6-tetrahydropyrimidin-2-yl)biphenyl-4-yl]-1H-indole, ... (4 entities in total)
• Functional Keywords: a2t2, dickerson and drew dodecamer, double helix, dna minor groove-ligand complex, dna minor groove binder, db1804, mg2+, dna
• Total number of polymer chains: 2
• Total formula weight: 7784.64

Authors

Wei, D.G.,Neidle, S. (deposition date: 2011-09-28, release date: 2012-09-12, Last modification date: 2024-02-28)

Primary citation

Wei, D.,Wilson, W.D.,Neidle, S.
Small-molecule binding to the DNA minor groove is mediated by a conserved water cluster.
J.Am.Chem.Soc., 135:1369-1377, 2013

PubMed Abstract: 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.

PubMed: 23276263
DOI: 10.1021/ja308952y

Experimental method

X-RAY DIFFRACTION (1.27 Å)