1d41: Difference between revisions

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[[Image:1d41.jpg|left|200px]]


{{Structure
==STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)==
|PDB= 1d41 |SIZE=350|CAPTION= <scene name='initialview01'>1d41</scene>, resolution 1.300&Aring;
<StructureSection load='1d41' size='340' side='right'caption='[[1d41]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
|SITE=
== Structural highlights ==
|LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene>
<table><tr><td colspan='2'>[[1d41]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D41 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D41 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]] 1.3&#8491;</td></tr>
|GENE=
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5CM:5-METHYL-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>5CM</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
}}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d41 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d41 OCA], [https://pdbe.org/1d41 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d41 RCSB], [https://www.ebi.ac.uk/pdbsum/1d41 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d41 ProSAT]</span></td></tr>
 
</table>
'''STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)'''
__TOC__
 
</StructureSection>
 
[[Category: Large Structures]]
==Overview==
[[Category: Ho PS]]
Methylation of cytosine bases at the C5 position has been known to stabilize Z-DNA. We had previously predicted from calculations of solvent-accessible surfaces that the methyl group at the same position of thymine has a destabilizing effect on Z-DNA. In the current studies, the sequence d(m5CGUAm5CG) has been crystallized and its structure solved as Z-DNA to 1.3-A resolution. A well-defined octahedral hexaaquomagnesium complex was observed to bridge the O4 oxygens of the adjacent uridine bases at the major groove surface, and four well-structured water molecules were found in the minor groove crevice at the d(UA) dinucleotide. These solvent interactions were not observed in the previously published Z-DNA structure of the analogous d(m5CGTAm5CG) sequence. A comparison of the thymine and uridine structures supports our prediction that demethylation of thymine bases helps to stabilize Z-DNA. A comparison of this d(UA)-containing Z-DNA structure with the analogous d(TA) structure shows that access of the O4 position is hindered by the C5 methyl of thymine due to steric and hydrophobic inhibition. In the absence of the methyl group, a magnesium-water complex binds to and slightly affects the structure of the Z-DNA major groove surface. This perturbation of the solvent structure at the major groove surface is translated into a much larger 1.41-A widening of the minor groove crevice, thereby allowing the specific binding of two water molecules at well-defined sites of each internal d(UA) base pair. Possible mechanisms by which modifications at the major groove surface of Z-DNA can affect the solvent properties of the minor groove crevice are discussed.
[[Category: Zhou G]]
 
==About this Structure==
1D41 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=1D41 OCA].  
 
==Reference==
Stabilization of Z-DNA by demethylation of thymine bases: 1.3-A single-crystal structure of d(m5CGUAm5CG)., Zhou GW, Ho PS, Biochemistry. 1990 Aug 7;29(31):7229-36. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2207101 2207101]
[[Category: Protein complex]]
[[Category: Ho, P S.]]
[[Category: Zhou, G.]]
[[Category: MG]]
[[Category: double helix]]
[[Category: modified]]
[[Category: z-dna]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 10:32:36 2008''

Latest revision as of 09:49, 7 February 2024

STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)STABILIZATION OF Z-DNA BY DEMETHYLATION OF THYMINE BASES: 1.3 ANGSTROMS SINGLE-CRYSTAL STRUCTURE OF D(M5CGUAM5CG)

Structural highlights

1d41 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.3Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

1d41, resolution 1.30Å

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