3LPV

X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link

Summary for 3LPV

• Entry DOI: 10.2210/pdb3lpv/pdb
• Related: 1AIO
• Descriptor: 5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3', 5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3', Cisplatin, ... (5 entities in total)
• Functional Keywords: cisplatin, dna
• Total number of polymer chains: 4
• Total formula weight: 15350.88

Authors

Todd, R.C.,Lippard, S.J. (deposition date: 2010-02-06, release date: 2010-08-11, Last modification date: 2023-09-06)

Primary citation

Todd, R.C.,Lippard, S.J.
Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link at 1.77A resolution.
J.Inorg.Biochem., 104:902-908, 2010

PubMed Abstract: We report the 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-A structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H(2)O)(6)](2+) ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.

PubMed: 20541266
DOI: 10.1016/j.jinorgbio.2010.04.005

Experimental method

X-RAY DIFFRACTION (1.77 Å)