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| - | [[Image:1dnf.jpg|left|200px]] | |
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| - | {{Structure
| + | ==EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)== |
| - | |PDB= 1dnf |SIZE=350|CAPTION= <scene name='initialview01'>1dnf</scene>, resolution 1.500Å
| + | <StructureSection load='1dnf' size='340' side='right'caption='[[1dnf]], [[Resolution|resolution]] 1.50Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UFP:5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>UFP</scene>
| + | <table><tr><td colspan='2'>[[1dnf]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DNF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNF 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]] 1.5Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UFP:5-FLUORO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>UFP</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=1dnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnf OCA], [https://pdbe.org/1dnf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnf RCSB], [https://www.ebi.ac.uk/pdbsum/1dnf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnf ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1dnf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnf OCA], [http://www.ebi.ac.uk/pdbsum/1dnf PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1dnf RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)'''
| + | [[Category: Aymami J]] |
| - | | + | [[Category: Coll M]] |
| - | | + | [[Category: Frederick CA]] |
| - | ==Overview==
| + | [[Category: Rich A]] |
| - | The chemotherapeutic agent 5-fluorouracil is a DNA base analogue which is known to incorporate into DNA in vivo. We have solved the structure of the oligonucleotide d(CGCGFG), where F is 5-fluorouracil (5FU). The DNA hexamer crystallizes in the Z-DNA conformation at two pH values with the 5FU forming a wobble base pair with guanine in both crystal forms. No evidence of the enol or ionized form of 5FU is found under either condition. The crystals diffracted X-rays to a resolution of 1.5 A and their structures have been refined to R-factors of 20.0% and 17.2%, respectively, for the pH = 7.0 and pH = 9.0 forms. By comparing this structure to that of d(CGCGCG) and d(CGCGTG), we were able to demonstrate that the backbone conformation of d(CGCGFG) is similar to that of the archetypal Z-DNA. The two F-G wobble base pairs in the duplex are structurally similar to the T-G base pairs both with respect to the DNA helix itself and its interactions with solvent molecules. In both cases water molecules associated with the wobble base pairs bridge between the bases and stabilize the structure. The fluorine in the 5FU base is hydrophobic and is not hydrogen bonded to any solvent molecules.
| + | [[Category: Saal D]] |
| - | | + | [[Category: Wang AH-J]] |
| - | ==About this Structure==
| + | |
| - | 1DNF 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=1DNF OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG)., Coll M, Saal D, Frederick CA, Aymami J, Rich A, Wang AH, Nucleic Acids Res. 1989 Feb 11;17(3):911-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2922276 2922276]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Aymami, J.]] | + | |
| - | [[Category: Coll, M.]] | + | |
| - | [[Category: Frederick, C A.]] | + | |
| - | [[Category: Rich, A.]] | + | |
| - | [[Category: Saal, D.]] | + | |
| - | [[Category: Wang, A H.J.]] | + | |
| - | [[Category: double helix]]
| + | |
| - | [[Category: mismatched]]
| + | |
| - | [[Category: modified]]
| + | |
| - | [[Category: z-dna]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:44:59 2008''
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