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| - | [[Image:446d.gif|left|200px]] | |
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| - | {{Structure
| + | ==STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS== |
| - | |PDB= 446d |SIZE=350|CAPTION= <scene name='initialview01'>446d</scene>, resolution 3.000Å
| + | <StructureSection load='446d' size='340' side='right'caption='[[446d]], [[Resolution|resolution]] 3.00Å' 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'>[[446d]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=446D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=446D 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]] 3Å</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=446d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=446d OCA], [https://pdbe.org/446d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=446d RCSB], [https://www.ebi.ac.uk/pdbsum/446d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=446d ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=446d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=446d OCA], [http://www.ebi.ac.uk/pdbsum/446d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=446d RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS'''
| + | [[Category: Abrescia NGA]] |
| - | | + | [[Category: Gonzaga LF]] |
| - | | + | [[Category: Huynh-Dinh T]] |
| - | ==Overview==
| + | [[Category: Malinina L]] |
| - | In this paper we explore the application of Ni2+to the crystallization of oligonucleotides. We have determined in this way the structure of a fully alternating (Y-R) decanucleotide d(CGTATATACG) by single crystal X-ray diffraction. This is the first oligonucleotide crystal structure with an alternating 5'-(TA)3-3' central part. Alternating oligonucleotides have a particular interest since they often have a unique structure. In this case the general conformation is B-like with an alternating twist and an end-to-end interaction which involves terminal guanines. The crystal belongs to space group P41212 with a = b = 52.46, c = 101.49 A. This packing imposes a 90 degrees crossing of the symmetry related helices. This is a new way of packing for decamers.The oligonucleotide structure is characterized by the specific association with seven nickel ions, involving the N7 atom of every guanine. One of the Ni2+ions is shared between two guanines of symmetry related molecules. Until now no oligonucleotide has been crystallized in the presence of this metal ion. A novel C.A.T triplet structure has also been tentatively identified.
| + | [[Category: Neidle S]] |
| - | | + | [[Category: Subirana JA]] |
| - | ==About this Structure==
| + | |
| - | 446D 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=446D OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Structure of the oligonucleotide d(CGTATATACG) as a site-specific complex with nickel ions., Abrescia NG, Malinina L, Fernandez LG, Huynh-Dinh T, Neidle S, Subirana JA, Nucleic Acids Res. 1999 Apr 1;27(7):1593-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/10075989 10075989]
| + | |
| - | [[Category: Protein complex]] | + | |
| - | [[Category: Abrescia, N G.A.]] | + | |
| - | [[Category: Gonzaga, L F.]] | + | |
| - | [[Category: Huynh-Dinh, T.]] | + | |
| - | [[Category: Malinina, L.]] | + | |
| - | [[Category: Neidle, S.]] | + | |
| - | [[Category: Subirana, J A.]] | + | |
| - | [[Category: nickel binding]]
| + | |
| - | [[Category: triple helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:27 2008''
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