1dnf
From Proteopedia
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|PDB= 1dnf |SIZE=350|CAPTION= <scene name='initialview01'>1dnf</scene>, resolution 1.500Å | |PDB= 1dnf |SIZE=350|CAPTION= <scene name='initialview01'>1dnf</scene>, resolution 1.500Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Saal, D.]] | [[Category: Saal, D.]] | ||
[[Category: Wang, A H.J.]] | [[Category: Wang, A H.J.]] | ||
| - | [[Category: MG]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: mismatched]] | [[Category: mismatched]] | ||
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[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''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 19:44:59 2008'' |
Revision as of 16:44, 30 March 2008
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| , resolution 1.500Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)
Overview
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.
About this Structure
1DNF is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:2922276
Page seeded by OCA on Sun Mar 30 19:44:59 2008
Categories: Protein complex | Aymami, J. | Coll, M. | Frederick, C A. | Rich, A. | Saal, D. | Wang, A H.J. | Double helix | Mismatched | Modified | Z-dna
