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| - | [[Image:2d25.gif|left|200px]] | |
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| - | {{Structure
| + | ==C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COMPARISON WITH C-C-A-G-G-C-C-T-G-G== |
| - | |PDB= 2d25 |SIZE=350|CAPTION= <scene name='initialview01'>2d25</scene>, resolution 1.750Å
| + | <StructureSection load='2d25' size='340' side='right'caption='[[2d25]], [[Resolution|resolution]] 1.75Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=5CM:5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE'>5CM</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>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
| + | <table><tr><td colspan='2'>[[2d25]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D25 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]] 1.75Å</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> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d25 OCA], [https://pdbe.org/2d25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d25 RCSB], [https://www.ebi.ac.uk/pdbsum/2d25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d25 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2d25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d25 OCA], [http://www.ebi.ac.uk/pdbsum/2d25 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2d25 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''C-C-A-G-G-C-M5C-T-G-G; HELICAL FINE STRUCTURE, HYDRATION, AND COMPARISON WITH C-C-A-G-G-C-C-T-G-G'''
| + | [[Category: Hahn M]] |
| - | | + | [[Category: Heinemann U]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | The self-complementary DNA duplex C-C-A-G-G-C-m5C-T-G-G has been refined against 1.75-A x-ray diffraction data to an R value of 17.4%. In the crystal of space group P6, 10-base pair DNA fragments with characteristic sequence-related fine structure stack end to end to form long antiparallel B-type double helices. As shown by a structure analysis at lower resolution (Heinemann, U., and Alings, C. (1991) EMBO J. 10, 35-43), the overall geometry of C-C-A-G-G-C-m5C-T-G-G is similar to that of the unmethylated analog C-C-A-G-G-C-C-T-G-G despite a different crystal environment. The present high resolution structure analysis permits a detailed comparison of the two duplexes and their hydration spheres. Helical parameters are significantly correlated between both molecules, with the exception of the base pair propeller. Sugar pucker and backbone torsion angles alpha, gamma, delta, and chi show similar mean values, but their individual values deviate significantly between duplexes. In contrast, torsion angles beta, epsilon, and zeta change along the strands of both duplexes in much the same way. The effect of single-site methylation on DNA conformation appears to be small and limited to the base pairs directly involved. Methylation tends to push base pairs toward the minor groove of the helix. A regular minor groove hydration pattern involves dual hydrogen bonding of water molecules to O-4' and base atoms of C-C-A-G-G-C-m5C-T-G-G.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2D25 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=2D25 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | C-C-A-G-G-C-m5C-T-G-G. Helical fine structure, hydration, and comparison with C-C-A-G-G-C-C-T-G-G., Heinemann U, Hahn M, J Biol Chem. 1992 Apr 15;267(11):7332-41. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1559976 1559976]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Hahn, M.]] | + | |
| - | [[Category: Heinemann, U.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: double helix]]
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| - | [[Category: modified]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:29:20 2008''
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