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| - | [[Image:1bd1.gif|left|200px]] | |
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| - | {{Structure
| + | ==CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA== |
| - | |PDB= 1bd1 |SIZE=350|CAPTION= <scene name='initialview01'>1bd1</scene>, resolution 1.600Å
| + | <StructureSection load='1bd1' size='340' side='right'caption='[[1bd1]], [[Resolution|resolution]] 1.60Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <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=TEA:TRIETHYLAMMONIUM+ION'>TEA</scene>
| + | <table><tr><td colspan='2'>[[1bd1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BD1 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]] 1.6Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TEA:TRIETHYLAMMONIUM+ION'>TEA</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=1bd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bd1 OCA], [https://pdbe.org/1bd1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bd1 RCSB], [https://www.ebi.ac.uk/pdbsum/1bd1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bd1 ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bd1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bd1 OCA], [http://www.ebi.ac.uk/pdbsum/1bd1 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bd1 RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA'''
| + | [[Category: Heinemann U]] |
| - | | + | |
| - | | + | |
| - | ==Overview==
| + | |
| - | The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography. At a nominal resolution of 1.6 A, the structure was refined to R = 16.9% using stereochemical restraints. The oligodeoxyribonucleotide forms a straight B-DNA double helix with crystallographic dyad symmetry and ten base-pairs per turn. In the crystal lattice, DNA fragments stack end-to-end along the c-axis to form continuous double helices. The overall helical structure and, notably, the groove dimensions of the decamer are more similar to standard, fiber diffraction-determined B-DNA than A-tract DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of the base-pairs along their long axes leads to a superposition of the base rings with neighboring carbonyl and amino functions. Three-center (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of the decamer. In their common sequence elements, d(CCAGGCCTGG) and the related G.A mismatch decamer d(CCAAGATTGG) show very similar three-dimensional structures, except that d(CCAGGCCTGG) appears to have a less regularly hydrated minor groove. The paucity of minor groove hydration in the center of the decamer may be a general feature of G/C-rich DNA and explain its relative instability in the B-form of DNA.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1BD1 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=1BD1 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | Crystallographic study of one turn of G/C-rich B-DNA., Heinemann U, Alings C, J Mol Biol. 1989 Nov 20;210(2):369-81. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2600970 2600970]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Heinemann, U.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 18:58:25 2008''
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