1jgr
From Proteopedia
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|PDB= 1jgr |SIZE=350|CAPTION= <scene name='initialview01'>1jgr</scene>, resolution 1.2Å | |PDB= 1jgr |SIZE=350|CAPTION= <scene name='initialview01'>1jgr</scene>, resolution 1.2Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TL:THALLIUM+(I)+ION'>TL</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1jgr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1jgr OCA], [http://www.ebi.ac.uk/pdbsum/1jgr PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1jgr RCSB]</span> | ||
}} | }} | ||
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[[Category: VanDerveer, D.]] | [[Category: VanDerveer, D.]] | ||
[[Category: Williams, L D.]] | [[Category: Williams, L D.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: TL]] | ||
[[Category: deoxyribonucleic acid]] | [[Category: deoxyribonucleic acid]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: thallium]] | [[Category: thallium]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:33:24 2008'' |
Revision as of 18:33, 30 March 2008
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| , resolution 1.2Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure Analysis of the B-DNA Dodecamer CGCGAATTCGCG with Thallium Ions.
Overview
Here we demonstrate that monovalent cations can localize around B-DNA in geometrically regular, sequence-specific sites in oligonucleotide crystals. Positions of monovalent ions were determined from high-resolution X-ray diffraction of DNA crystals grown in the presence of thallium(I) cations (Tl(+)). Tl(+) has previously been shown to be a useful K(+) mimic. Tl(+) positions determined by refinement of model to data are consistent with positions determined using isomorphous F(Tl) - F(K) difference Fouriers and anomalous difference Fouriers. None of the observed Tl(+) sites surrounding CGCGAATTCGCG are fully occupied by Tl(+) ions. The most highly occupied sites, located within the G-tract major groove, have estimated occupancies ranging from 20% to 35%. The occupancies of the minor groove sites are estimated to be around 10%. The Tl(+) positions in general are not in direct proximity to phosphate groups. The A-tract major groove appears devoid of localized cations. The majority of the observed Tl(+) ions interact with a single duplex and so are not engaged in lattice interactions or crystal packing. The locations of the cation sites are dictated by coordination geometry, electronegative potential, avoidance of electropositive amino groups, and cation-pi interactions. It appears that partially dehydrated monovalent cations, hydrated divalent cations, and polyamines compete for a common binding region on the floor of the G-tract major groove.
About this Structure
1JGR is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Locating monovalent cations in the grooves of B-DNA., Howerton SB, Sines CC, VanDerveer D, Williams LD, Biochemistry. 2001 Aug 28;40(34):10023-31. PMID:11513580
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