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PDBsum entry 1a2e
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dna_rna ligands links
DNA PDB id
1a2e

 

 

 

 

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Contents
DNA/RNA
Ligands
CPT
Waters ×92
PDB id:
1a2e
Name: DNA
Title: Crystal structure of a double-stranded DNA decamer containing a cisplatin interstrand cross-link adduct
Structure: DNA (5'-d( Cp Cp Tp Cp Gp Cp Tp Cp Tp C)-3'). Chain: a. Engineered: yes. Other_details: pt(cpt) crosslinks n7(g5) and n7(g15). DNA (5'-d( Gp Ap Gp Ap Gp Cp Gp Ap Gp G)-3'). Chain: b. Engineered: yes. Other_details: pt(cpt) crosslinks n7(g5) and n7(g15)
Source: Synthetic: yes. Synthetic: yes
Biol. unit: Monomer (from PDB file)
Resolution:
1.63Å     R-factor:   0.169     R-free:   0.203
Authors: F.Coste,C.Zelwer
Key ref: F.Coste et al. (1999). Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site. Nucleic Acids Res, 27, 1837-1846. PubMed id: 10101191
Date:
05-Jan-98     Release date:   12-Apr-99    
 Headers
 References

DNA/RNA chains
  C-C-T-C-G-C-T-C-T-C 10 bases
  G-A-G-A-G-C-G-A-G-G 10 bases

 

 
Nucleic Acids Res 27:1837-1846 (1999)
PubMed id: 10101191  
 
 
Crystal structure of a double-stranded DNA containing a cisplatin interstrand cross-link at 1.63 A resolution: hydration at the platinated site.
F.Coste, J.M.Malinge, L.Serre, W.Shepard, M.Roth, M.Leng, C.Zelwer.
 
  ABSTRACT  
 
cis-diamminedichloroplatinum (II) (cisplatin) is a powerful anti-tumor drug whose target is cellular DNA. In the reaction between DNA and cisplatin, covalent intrastrand and interstrand cross-links (ICL) are formed. Two solution structures of the ICL have been published recently. In both models the double-helix is bent and unwound but with significantly different angle values. We solved the crystal structure at 100K of a double-stranded DNA decamer containing a single cisplatin ICL, using the anomalous scattering (MAD) of platinum as a unique source of phase information. We found 47 degrees for double-helix bending and 70 degrees for unwinding in agreement with previous electrophoretic assays. The crystals are stabilized by intermolecular contacts involving two cytosines extruded from the double-helix, one of which makes a triplet with a terminal G.C pair. The platinum coordination is nearly square and the platinum residue is embedded into a cage of nine water molecules linked to the cross-linked guanines, to the two amine groups, and to the phosphodiester backbone through other water molecules. This water molecule organization is discussed in relation with the chemical stability of the ICL.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
21082220 G.Caron, M.Ravera, and G.Ermondi (2011).
Molecular Interaction Fields (MIFs) to Predict Lipophilicity and ADME Profile of Antitumor Pt(II) Complexes.
  Pharm Res, 28, 640-646.  
21421126 M.Ravera, E.Gabano, M.Sardi, G.Ermondi, G.Caron, M.J.McGlinchey, H.Müller-Bunz, E.Monti, M.B.Gariboldi, and D.Osella (2011).
Synthesis, characterization, structure, molecular modeling studies and biological activity of sterically crowded Pt(II) complexes containing bis(imidazole) ligands.
  J Inorg Biochem, 105, 400-409.  
20736180 S.Komeda, T.Moulaei, M.Chikuma, A.Odani, R.Kipping, N.P.Farrell, and L.D.Williams (2011).
The phosphate clamp: a small and independent motif for nucleic acid backbone recognition.
  Nucleic Acids Res, 39, 325-336.  
20730555 A.Guainazzi, and O.D.Schärer (2010).
Using synthetic DNA interstrand crosslinks to elucidate repair pathways and identify new therapeutic targets for cancer chemotherapy.
  Cell Mol Life Sci, 67, 3683-3697.  
  20725618 G.Lenglet, and M.H.David-Cordonnier (2010).
DNA-Destabilizing Agents as an Alternative Approach for Targeting DNA: Mechanisms of Action and Cellular Consequences.
  J Nucleic Acids, 2010, 0.  
20694266 J.B.Mangrum, and N.P.Farrell (2010).
Excursions in polynuclear platinum DNA binding.
  Chem Commun (Camb), 46, 6640-6650.  
20727966 K.Johansson, J.Järvliden, V.Gogvadze, and R.Morgenstern (2010).
Multiple roles of microsomal glutathione transferase 1 in cellular protection: a mechanistic study.
  Free Radic Biol Med, 49, 1638-1645.  
19364127 G.Zhu, and S.J.Lippard (2009).
Photoaffinity labeling reveals nuclear proteins that uniquely recognize cisplatin-DNA interstrand cross-links.
  Biochemistry, 48, 4916-4925.  
19350599 J.Zhu, Y.Zhao, Y.Zhu, Z.Wu, M.Lin, W.He, Y.Wang, G.Chen, L.Dong, J.Zhang, Y.Lu, and Z.Guo (2009).
DNA cross-linking patterns induced by an antitumor-active trinuclear platinum complex and comparison with its dinuclear analogue.
  Chemistry, 15, 5245-5253.  
  20046924 R.C.Todd, and S.J.Lippard (2009).
Inhibition of transcription by platinum antitumor compounds.
  Metallomics, 1, 280-291.  
20161688 S.M.Aris, and N.P.Farrell (2009).
Towards Antitumor Active trans-Platinum Compounds.
  Eur J Inorg Chem, 2009, 1293.  
19415349 Y.Qu, M.C.Tran, and N.P.Farrell (2009).
Structural consequences of a 3'-->3' DNA interstrand cross-link by a trinuclear platinum complex: unique formation of two such cross-links in a 10-mer duplex.
  J Biol Inorg Chem, 14, 969-977.  
18537208 J.Zhang, D.S.Thomas, S.J.Berners-Price, and N.Farrell (2008).
Effects of geometric isomerism and anions on the kinetics and mechanism of the stepwise formation of long-range DNA interstrand cross-links by dinuclear platinum antitumor complexes.
  Chemistry, 14, 6391-6405.  
18322710 O.Bradác, T.Zimmermann, and J.V.Burda (2008).
Comparison of the electronic properties, and thermodynamic and kinetic parameters of the aquation of selected platinum(II) derivatives with their anticancer IC50 indexes.
  J Mol Model, 14, 705-716.  
17329374 K.Chválová, V.Brabec, and J.Kaspárková (2007).
Mechanism of the formation of DNA-protein cross-links by antitumor cisplatin.
  Nucleic Acids Res, 35, 1812-1821.  
17375936 M.C.Swenson, S.R.Paranawithana, P.S.Miller, and C.L.Kielkopf (2007).
Structure of a DNA repair substrate containing an alkyl interstrand cross-link at 1.65 A resolution.
  Biochemistry, 46, 4545-4553.
PDB code: 2oks
17024406 M.Pavelka, and J.V.Burda (2007).
Pt-bridges in various single-strand and double-helix DNA sequences. DFT and MP2 study of the cisplatin coordination with guanine, adenine, and cytosine.
  J Mol Model, 13, 367-379.  
17096663 P.Lehoczký, P.J.McHugh, and M.Chovanec (2007).
DNA interstrand cross-link repair in Saccharomyces cerevisiae.
  FEMS Microbiol Rev, 31, 109-133.  
16464006 D.M.Noll, T.M.Mason, and P.S.Miller (2006).
Formation and repair of interstrand cross-links in DNA.
  Chem Rev, 106, 277-301.  
15643666 A.H.Velders, A.C.Hotze, and J.Reedijk (2005).
Ligands rock & roll: stepwise twisting of two cis-coordinated lopsided N-heterocycles in an octahedral bis(2-phenylazopyridine)-ruthenium(II) complex with seven atropisomers.
  Chemistry, 11, 1325-1340.  
15516529 A.Sischka, K.Toensing, R.Eckel, S.D.Wilking, N.Sewald, R.Ros, and D.Anselmetti (2005).
Molecular mechanisms and kinetics between DNA and DNA binding ligands.
  Biophys J, 88, 404-411.  
15841473 J.V.Burda, M.Zeizinger, and J.Leszczynski (2005).
Hydration process as an activation of trans- and cisplatin complexes in anticancer treatment. DFT and ab initio computational study of thermodynamic and kinetic parameters.
  J Comput Chem, 26, 907-914.  
15155847 N.B.Edfeldt, E.A.Harwood, S.T.Sigurdsson, P.B.Hopkins, and B.R.Reid (2004).
Solution structure of a nitrous acid induced DNA interstrand cross-link.
  Nucleic Acids Res, 32, 2785-2794.
PDB codes: 1s9n 1s9o
15155848 N.B.Edfeldt, E.A.Harwood, S.T.Sigurdsson, P.B.Hopkins, and B.R.Reid (2004).
Sequence context effect on the structure of nitrous acid induced DNA interstrand cross-links.
  Nucleic Acids Res, 32, 2795-2801.  
12939790 L.J.Ming (2003).
Structure and function of "metalloantibiotics".
  Med Res Rev, 23, 697-762.  
12626701 S.Redon, S.Bombard, M.A.Elizondo-Riojas, and J.C.Chottard (2003).
Platinum cross-linking of adenines and guanines on the quadruplex structures of the AG3(T2AG3)3 and (T2AG3)4 human telomere sequences in Na+ and K+ solutions.
  Nucleic Acids Res, 31, 1605-1613.  
11856828 F.Coste, W.Shepard, and C.Zelwer (2002).
Description of ordered solvent molecules in a platinated decanucleotide duplex refined at 1.6A resolution against experimental MAD phases.
  Acta Crystallogr D Biol Crystallogr, 58, 431-440.
PDB code: 1i1p
11867468 N.Foloppe, B.Hartmann, L.Nilsson, and A.D.MacKerell (2002).
Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study.
  Biophys J, 82, 1554-1569.  
11344319 R.Cerdan, D.Payet, J.C.Yang, A.A.Travers, and D.Neuhaus (2001).
HMG-D complexed to a bulge DNA: an NMR model.
  Protein Sci, 10, 504-518.
PDB code: 1e7j
11202359 R.Ghosh, L.Paniker, and D.L.Mitchell (2001).
Bound transcription factor suppresses photoproduct formation in the NF-kappa B promoter.
  Photochem Photobiol, 73, 1-5.  
10561579 H.Loskotová, and V.Brabec (1999).
DNA interactions of cisplatin tethered to the DNA minor groove binder distamycin.
  Eur J Biochem, 266, 392-402.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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