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| <StructureSection load='1uhx' size='340' side='right'caption='[[1uhx]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1uhx' size='340' side='right'caption='[[1uhx]], [[Resolution|resolution]] 2.00Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
- | <table><tr><td colspan='2'>[[1uhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UHX FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UHX FirstGlance]. <br> |
- | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
- | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr> |
- | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1uhy|1uhy]]</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=1uhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uhx OCA], [https://pdbe.org/1uhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uhx RCSB], [https://www.ebi.ac.uk/pdbsum/1uhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uhx ProSAT]</span></td></tr> |
- | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uhx OCA], [http://pdbe.org/1uhx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uhx RCSB], [http://www.ebi.ac.uk/pdbsum/1uhx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uhx ProSAT]</span></td></tr> | + | |
| </table> | | </table> |
| <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| </StructureSection> | | </StructureSection> |
| [[Category: Large Structures]] | | [[Category: Large Structures]] |
- | [[Category: Fujita, K]] | + | [[Category: Fujita K]] |
- | [[Category: Kondo, J]] | + | [[Category: Kondo J]] |
- | [[Category: Sunami, T]] | + | [[Category: Sunami T]] |
- | [[Category: Takenaka, A]] | + | [[Category: Takenaka A]] |
- | [[Category: Umeda, S I]] | + | [[Category: Umeda SI]] |
- | [[Category: Base-intercalated duplex]]
| + | |
- | [[Category: Base-intercalated motif]]
| + | |
- | [[Category: Deoxyribonucleic acid]]
| + | |
- | [[Category: Dna]]
| + | |
- | [[Category: Sheared g:a pair]]
| + | |
| Structural highlights
1uhx is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| Method: | X-ray diffraction, Resolution 2Å |
Ligands: | , , , , |
Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.
X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.,Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:14646150[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A. X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue. J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:14646150
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