446d
From Proteopedia
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|PDB= 446d |SIZE=350|CAPTION= <scene name='initialview01'>446d</scene>, resolution 3.000Å | |PDB= 446d |SIZE=350|CAPTION= <scene name='initialview01'>446d</scene>, resolution 3.000Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NI:NICKEL (II) ION'>NI</scene> | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Neidle, S.]] | [[Category: Neidle, S.]] | ||
[[Category: Subirana, J A.]] | [[Category: Subirana, J A.]] | ||
| - | [[Category: NI]] | ||
[[Category: nickel binding]] | [[Category: nickel binding]] | ||
[[Category: triple helix]] | [[Category: triple helix]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:37:27 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 3.000Å | |||||||
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| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF THE OLIGONUCLEOTIDE D(CGTATATACG) AS A SITE SPECIFIC COMPLEX WITH NICKEL IONS
Overview
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.
About this Structure
446D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:10075989
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