1g8u

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[[Image:1g8u.gif|left|200px]]
[[Image:1g8u.gif|left|200px]]
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{{Structure
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|PDB= 1g8u |SIZE=350|CAPTION= <scene name='initialview01'>1g8u</scene>, resolution 1.85&Aring;
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The line below this paragraph, containing "STRUCTURE_1g8u", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=UFR:2&#39;-DEOXY-5-FORMYLURIDINE+5&#39;-(DIHYDROGEN+PHOSPHATE)'>UFR</scene>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|ACTIVITY=
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or leave the SCENE parameter empty for the default display.
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|GENE=
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|DOMAIN=
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{{STRUCTURE_1g8u| PDB=1g8u | SCENE= }}
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|RELATEDENTRY=
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1g8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1g8u OCA], [http://www.ebi.ac.uk/pdbsum/1g8u PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1g8u RCSB]</span>
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}}
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'''MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA'''
'''MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA'''
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==About this Structure==
==About this Structure==
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1G8U 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=1G8U OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1G8U OCA].
==Reference==
==Reference==
Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?, Tsunoda M, Karino N, Ueno Y, Matsuda A, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):345-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173500 11173500]
Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?, Tsunoda M, Karino N, Ueno Y, Matsuda A, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):345-8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11173500 11173500]
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[[Category: Protein complex]]
 
[[Category: Karino, N.]]
[[Category: Karino, N.]]
[[Category: Matsuda, A.]]
[[Category: Matsuda, A.]]
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[[Category: Tsunoda, M.]]
[[Category: Tsunoda, M.]]
[[Category: Ueno, Y.]]
[[Category: Ueno, Y.]]
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[[Category: deoxyribonucleic acid]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: dna damage,b-dna]]
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[[Category: Dna damage,b-dna]]
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[[Category: double helix]]
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[[Category: Double helix]]
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[[Category: formyluridine]]
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[[Category: Formyluridine]]
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[[Category: modified nucleotide]]
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[[Category: Modified nucleotide]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 17:17:20 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 20:39:02 2008''
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Revision as of 14:17, 2 May 2008

Image:1g8u.gif

Template:STRUCTURE 1g8u

MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGAATF5UCGCG):5-FORMYLURIDINE/ ADENOSINE BASE-PAIRS IN B-DNA


Overview

To investigate the role of divalent cations in crystal packing, four different crystals of a Dickerson-type dodecamer with the sequence d(CGCGAATXCGCG), containing 2'-deoxy-5-formyluridine at X, were obtained under several conditions with and without divalent cations. The crystal structures are all isomorphous. The octahedrally hydrated magnesium cations found in the major groove cement the two neighbouring duplexes along the b axis. In the Mg(2+)-free crystals, a five-membered ring of water molecules occupies the same position as the magnesium site and connects the two duplexes similarly to the hydrated Mg(2+) ion. It has been concluded that water molecules can take the place of the hydrated magnesium cation in crystallization, but the magnesium cation is more effective and gives X-ray diffraction at slightly higher resolution. In all four crystals, the 5-formyluracil residues form the canonical Watson-Crick pair with adenine residues.

About this Structure

Full crystallographic information is available from OCA.

Reference

Crystallization and preliminary X-ray analysis of a DNA dodecamer containing 2'-deoxy-5-formyluridine; what is the role of magnesium cation in crystallization of Dickerson-type DNA dodecamers?, Tsunoda M, Karino N, Ueno Y, Matsuda A, Takenaka A, Acta Crystallogr D Biol Crystallogr. 2001 Feb;57(Pt 2):345-8. PMID:11173500 Page seeded by OCA on Fri May 2 17:17:20 2008

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