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| - | [[Image:1g3v.gif|left|200px]]<br /><applet load="1g3v" size="350" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1g3v, resolution 3.1Å" /> | |
| - | '''CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2'''<br /> | |
| | | | |
| - | ==Overview== | + | ==CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2== |
| - | The aim of this study was to clarify whether Ni2+ ions could bind to guanine bases in a standard B-DNA duplex and eventually induce a B-->Z transition. We have determined by X-ray crystallography at 3.1 A resolution the structure of the alternating deoxynucleotide d(CGTGTACACG), which contains both internal and terminal guanines. The duplex is in the B form. It is shown that nickel ions bind selectively to the N7 atom of guanine 10, which is in an extra-helical position, and guanine 2, which is in the terminal position of the duplex. It does not bind to guanine 4, which lies within a standard B-DNA tract. This simple but unambiguous result proves that nickel ions select between different guanines via steric accessibility. Guanine-Ni2+-guanine bridges among symmetry-related duplexes have also been found. These bridges may explain why Ni2+ ions may act either as a precipitant or a renaturing agent for DNA under certain conditions. The biochemical interaction of nickel with DNA can thus be related to its capacity to specifically bind to B-DNA regions with exposed guanines. Also, from the structural point of view, we have found a terminal cytosine, which forms a C.G:C reverse-Hoogsteen triple structure with a base pair of a neighbor duplex. This type of triplet is seldom found and is here described for the first time for a DNA structure.
| + | <StructureSection load='1g3v' size='340' side='right'caption='[[1g3v]], [[Resolution|resolution]] 3.10Å' scene=''> |
| - | | + | == Structural highlights == |
| - | ==About this Structure==
| + | <table><tr><td colspan='2'>[[1g3v]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1G3V FirstGlance]. <br> |
| - | 1G3V is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NI:'>NI</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3V OCA].
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.1Å</td></tr> |
| - | | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene></td></tr> |
| - | ==Reference==
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1g3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3v OCA], [https://pdbe.org/1g3v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1g3v RCSB], [https://www.ebi.ac.uk/pdbsum/1g3v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1g3v ProSAT]</span></td></tr> |
| - | Nickel-guanine interactions in DNA: crystal structure of nickel-d[CGTGTACACG]2., Abrescia NA, Huynh-Dinh T, Subirana JA, J Biol Inorg Chem. 2002 Jan;7(1-2):195-9. Epub 2001 Aug 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11862555 11862555]
| + | </table> |
| - | [[Category: Protein complex]] | + | __TOC__ |
| - | [[Category: Abrescia, N G.A.]]
| + | </StructureSection> |
| - | [[Category: Subirana, J A.]] | + | [[Category: Large Structures]] |
| - | [[Category: NI]] | + | [[Category: Abrescia NGA]] |
| - | [[Category: b-dna]] | + | [[Category: Subirana JA]] |
| - | [[Category: nickel binding]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:45:46 2008''
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