1z5t
From Proteopedia
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|PDB= 1z5t |SIZE=350|CAPTION= <scene name='initialview01'>1z5t</scene>, resolution 1.600Å | |PDB= 1z5t |SIZE=350|CAPTION= <scene name='initialview01'>1z5t</scene>, resolution 1.600Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=SPM:SPERMINE'>SPM</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=SPM:SPERMINE'>SPM</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene>, <scene name='pdbligand=ZDU:5-(3-AMINOPROPYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>ZDU</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1z5t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1z5t OCA], [http://www.ebi.ac.uk/pdbsum/1z5t PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1z5t RCSB]</span> | ||
}} | }} | ||
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[[Category: Watkins, D.]] | [[Category: Watkins, D.]] | ||
[[Category: Williams, L D.]] | [[Category: Williams, L D.]] | ||
| - | [[Category: SPM]] | ||
| - | [[Category: TL]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: cation]] | [[Category: cation]] | ||
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[[Category: tl+]] | [[Category: tl+]] | ||
| - | ''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 01:29:30 2008'' |
Revision as of 22:29, 30 March 2008
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| , resolution 1.600Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of [d(CGCGAA(Z3dU)(Z3dU)CGCG)]2, Z3dU:5-(3-aminopropyl)-2'-deoxyuridine, in presence of thallium I.
Overview
Here, we describe the 1.6-A X-ray structure of the DDD (Dickerson-Drew dodecamer), which has been covalently modified by the tethering of four cationic charges. This modified version of the DDD, called here the DDD(4+), is composed of [d(CGCGAAXXCGCG)](2), where X is effectively a thymine residue linked at the 5 position to an n-propyl-amine. The structure was determined from crystals soaked with thallium(I), which has been broadly used as a mimic of K(+) in X-ray diffraction experiments aimed at determining positions of cations adjacent to nucleic acids. Three of the tethered cations are directed radially out from the DNA. The radially directed tethered cations do not appear to induce structural changes or to displace counterions. One of the tethered cations is directed in the 3' direction, toward a phosphate group near one end of the duplex. This tethered cation appears to interact electrostatically with the DNA. This interaction is accompanied by changes in helical parameters rise, roll, and twist and by a displacement of the backbone relative to a control oligonucleotide. In addition, these interactions appear to be associated with displacement of counterions from the major groove of the DNA.
About this Structure
1Z5T is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure of B-DNA with cations tethered in the major groove., Moulaei T, Maehigashi T, Lountos GT, Komeda S, Watkins D, Stone MP, Marky LA, Li JS, Gold B, Williams LD, Biochemistry. 2005 May 24;44(20):7458-68. PMID:15895989
Page seeded by OCA on Mon Mar 31 01:29:30 2008
Categories: Protein complex | Gold, B. | Komeda, S. | Li, J S. | Lountos, G T. | Maehigashi, T. | Marky, L A. | Moulaei, T. | Stone, M P. | Watkins, D. | Williams, L D. | B-dna | Cation | Modified dna | Modified thymine | Thallium | Tl+
