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1d40

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[[Image:1d40.gif|left|200px]]<br /><applet load="1d40" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1d40, resolution 1.300&Aring;" />
 
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'''BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS SINGLE CRYSTAL STRUCTURE OF D(M5CGUAM5CG) IN THE PRESENCE OF CUCL2'''<br />
 
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==Overview==
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==BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS SINGLE CRYSTAL STRUCTURE OF D(M5CGUAM5CG) IN THE PRESENCE OF CUCL2==
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The single crystal structure of d(m5CGUAm5CG) soaked with copper(II) chloride was solved to atomic (1.3 A) resolution to study the base specificity of copper binding to double-stranded DNA. In the present copper(II) chloride-soaked structure, four crystallographically unique copper(II) complexes were observed bound to five of the six purine bases in the hexamer duplex. Covalent copper(II) binding occurred at N-7 of all four guanine bases and at one of the two adenine bases in the DNA duplex. Copper binding was not observed at the position (Ade4) located in an open solvent channel, whereas the second adenine site (Ade10) shared a complex with a guanine residue (Gua12) of a neighboring symmetry-related hexamer. The coordination geometries and distribution of these copper(II) complexes at the guanine bases in the crystal were comparable to the analogous sites in the isomorphous copper(II) chloride-soaked d(CGCGCG) crystal (Kagawa, T., Geierstanger, B. H., Wang, A. H.-J., and Ho, P.S. (1991) J. Biol. Chem. 266, 20175-20184). Thus, the decreased copper(II) binding affinity for Ade4 was not an artifact of crystal packing, but is intrinsic to the chemical properties of this purine base in duplex DNA. This suggests that the adenine bases in dilute solutions of Z-DNA and more generally other duplex DNA conformations are not susceptible to copper(II) modification. Thus, preferential copper(II) binding at guanine bases over adenine bases in double-stranded DNA may explain the observed specificity of copper(II)-induced oxidative DNA damage near guanine residues (Yamamoto, K., and Kawanishi, S. (1989) J. Biol. Chem. 264, 15435-15440; Sagripanti, J.-L., and Kraemer, K. H. (1989) J. Biol. Chem. 264, 1729-1734). The sharing of a single copper(II) complex by Ade10 and Gua12 of an adjacent hexamer suggests that additional and perhaps specific DNA-DNA interactions, as may be found in the densely packed environment of the nuclear matrix in the cell, may render N-7 of adenine bases prone to copper(II) modification.
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<StructureSection load='1d40' size='340' side='right'caption='[[1d40]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1d40]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D40 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D40 FirstGlance]. <br>
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1D40 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=CU:'>CU</scene> and <scene name='pdbligand=CUL:'>CUL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D40 OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUL:COPPER+(II)+CHLORIDE'>CUL</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d40 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d40 OCA], [https://pdbe.org/1d40 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d40 RCSB], [https://www.ebi.ac.uk/pdbsum/1d40 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d40 ProSAT]</span></td></tr>
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Base-specific binding of copper(II) to Z-DNA. The 1.3-A single crystal structure of d(m5CGUAm5CG) in the presence of CuCl2., Geierstanger BH, Kagawa TF, Chen SL, Quigley GJ, Ho PS, J Biol Chem. 1991 Oct 25;266(30):20185-91. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1939079 1939079]
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</table>
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[[Category: Protein complex]]
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__TOC__
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[[Category: Chen, S L.]]
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</StructureSection>
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[[Category: Geierstanger, B H.]]
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[[Category: Large Structures]]
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[[Category: Ho, P S.]]
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[[Category: Chen S-L]]
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[[Category: Kagawa, T F.]]
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[[Category: Geierstanger BH]]
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[[Category: Quigley, G J.]]
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[[Category: Ho PS]]
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[[Category: CU]]
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[[Category: Kagawa TF]]
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[[Category: CUL]]
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[[Category: Quigley GJ]]
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[[Category: double helix]]
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[[Category: modified]]
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[[Category: z-dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:44 2008''
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Current revision

BASE SPECIFIC BINDING OF COPPER(II) TO Z-DNA: THE 1.3-ANGSTROMS SINGLE CRYSTAL STRUCTURE OF D(M5CGUAM5CG) IN THE PRESENCE OF CUCL2

PDB ID 1d40

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