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383d

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[[Image:383d.gif|left|200px]]<br /><applet load="383d" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="383d, resolution 1.700&Aring;" />
 
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'''Hydration and recognition of methylated CPG steps in DNA'''<br />
 
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==Overview==
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==Hydration and recognition of methylated CPG steps in DNA==
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The analysis of the hydration pattern around methylated CpG steps in three high resolution (1.7, 2.15 and 2.2 A) crystal structures of A-DNA decamers reveals that the methyl groups of cytosine residues are well hydrated. In comparing the native structure with two structurally distinct forms of the decamer d(CCGCCGGCGG) fully methylated at its CpG steps, this study shows also that in certain structural and sequence contexts, the methylated cytosine base can be more hydrated that the unmodified one. These water molecules seem to be stabilized in front of the methyl group through the formation C-H...O interactions. In addition, these structures provide the first observation of magnesium cations bound to the major groove of A-DNA and reveal two distinct modes of metal binding in methylated and native duplexes. These findings suggest that methylated cytosine bases could be recognized by protein or DNA polar residues through their tightly bound water molecules.
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<StructureSection load='383d' size='340' side='right'caption='[[383d]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[383d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=383D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=383D FirstGlance]. <br>
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383D is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=MG:'>MG</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=383D OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<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>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=383d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=383d OCA], [https://pdbe.org/383d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=383d RCSB], [https://www.ebi.ac.uk/pdbsum/383d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=383d ProSAT]</span></td></tr>
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Hydration and recognition of methylated CpG steps in DNA., Mayer-Jung C, Moras D, Timsit Y, EMBO J. 1998 May 1;17(9):2709-18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9564052 9564052]
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</table>
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[[Category: Single protein]]
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__TOC__
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[[Category: Mayer-Jung, C.]]
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</StructureSection>
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[[Category: Moras, D.]]
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[[Category: Large Structures]]
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[[Category: Timsit, Y.]]
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[[Category: Mayer-Jung C]]
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[[Category: MG]]
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[[Category: Moras D]]
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[[Category: a-dna]]
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[[Category: Timsit Y]]
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[[Category: double helix]]
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[[Category: modified deoxyribonucleic acid]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:02:31 2008''
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Current revision

Hydration and recognition of methylated CPG steps in DNA

PDB ID 383d

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