417d
From Proteopedia
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|PDB= 417d |SIZE=350|CAPTION= <scene name='initialview01'>417d</scene>, resolution 1.500Å | |PDB= 417d |SIZE=350|CAPTION= <scene name='initialview01'>417d</scene>, resolution 1.500Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=C46:6H,8H-3,4-DIHYDROPYRIMIDO[4,5-C][1,2]OXAZIN-7-0NE(CYTIDINE)-5'-MONOPHOSPHATE'>C46</scene>, <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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=417d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=417d OCA], [http://www.ebi.ac.uk/pdbsum/417d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=417d RCSB]</span> | ||
}} | }} | ||
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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 Mon Mar 31 05:36:55 2008'' |
Revision as of 02:36, 31 March 2008
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| , resolution 1.500Å | |||||||
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| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
A THYMINE-LIKE BASE ANALOGUE FORMS WOBBLE PAIRS WITH ADENINE
Overview
The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inconsistent with other evidence from hybridisation and NMR studies of P-containing oligonucleotides, which suggests that, while P can form stable base-pairs with either A or G, thymine-like properties are more pronounced. Thermal denaturation experiments over a range of solution pH values indicate that protonation of the P.A base-pairs is unlikely to be responsible for the anomalous behaviour. No specific crystal packing effects can be identfied as an explanation, and it is concluded that base stacking and other interactions between nucleotide residues in Z-DNA are responsible.
About this Structure
417D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex., Schuerman GS, Van Meervelt L, Loakes D, Brown DM, Kong Thoo Lin P, Moore MH, Salisbury SA, J Mol Biol. 1998 Oct 9;282(5):1005-11. PMID:9753550
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