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| - | [[Image:1g3v.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2== |
| - | |PDB= 1g3v |SIZE=350|CAPTION= <scene name='initialview01'>1g3v</scene>, resolution 3.1Å
| + | <StructureSection load='1g3v' size='340' side='right'caption='[[1g3v]], [[Resolution|resolution]] 3.10Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=NI:NICKEL+(II)+ION'>NI</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </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> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g3v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g3v OCA], [http://www.ebi.ac.uk/pdbsum/1g3v PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1g3v RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTAL STRUCTURE OF NICKEL-D[CGTGTACACG]2'''
| + | [[Category: Abrescia NGA]] |
| - | | + | [[Category: Subirana JA]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1G3V is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G3V OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/11862555 11862555]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Abrescia, N G.A.]] | + | |
| - | [[Category: Subirana, J A.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: nickel binding]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:36:02 2008''
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