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| - | [[Image:2dnd.jpg|left|200px]] | |
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| - | {{Structure
| + | ==A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX WITH DISTAMYCIN== |
| - | |PDB= 2dnd |SIZE=350|CAPTION= <scene name='initialview01'>2dnd</scene>, resolution 2.200Å
| + | <StructureSection load='2dnd' size='340' side='right'caption='[[2dnd]], [[Resolution|resolution]] 2.20Å' 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=DMY:DISTAMYCIN+A'>DMY</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <table><tr><td colspan='2'>[[2dnd]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DND OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DND 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]] 2.2Å</td></tr> |
| - | |GENE=
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DMY:DISTAMYCIN+A'>DMY</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=2dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dnd OCA], [https://pdbe.org/2dnd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dnd RCSB], [https://www.ebi.ac.uk/pdbsum/2dnd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dnd ProSAT]</span></td></tr> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2dnd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dnd OCA], [http://www.ebi.ac.uk/pdbsum/2dnd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2dnd RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''A BIFURCATED HYDROGEN-BONDED CONFORMATION IN THE D(A.T) BASE PAIRS OF THE DNA DODECAMER D(CGCAAATTTGCG) AND ITS COMPLEX WITH DISTAMYCIN'''
| + | [[Category: Coll M]] |
| - | | + | [[Category: Frederick CA]] |
| - | | + | [[Category: Rich A]] |
| - | ==Overview==
| + | [[Category: Wang AH-J]] |
| - | The crystal structures of d(CGCA3T3GCG) complex to the antitumor drug distamycin and the DNA fragment alone were solved by x-ray diffraction at 2.2 and 2.5 A resolution, respectively. The drug lies in the narrow minor groove near the center of the B-DNA fragment covering 5 of the 6 A.T base pairs. It is bound to the DNA by hydrogen bonding, van der Waals, and electrostatic interactions. In addition, the DNA was found to have an unusual conformation in the (dA)3.(dT)3 regions. These base pairs have a high positive propeller twist so that in the major groove the adenine amino group is located intermediate between the carbonyl O-4 groups of two adjacent thymines of the opposite strand, making bifurcated hydrogen bonds to the two thymine residues. This suggests a model to explain the unusual properties of poly-(dA).poly(dT) in which a modified B conformation is associated with a large propeller twist of the bases and a set of continuous bifurcating hydrogen bonds along the major groove, which may provide incremental stability to these segments. In addition, shorter segments of (dA)3-6.(dT)3-6 may have this conformation in the midst of B-DNA and stabilize bends in the DNA that may be associated with stacking on one of the high propeller-twisted bases at the ends of these segments.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 2DND 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=2DND OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | A bifurcated hydrogen-bonded conformation in the d(A.T) base pairs of the DNA dodecamer d(CGCAAATTTGCG) and its complex with distamycin., Coll M, Frederick CA, Wang AH, Rich A, Proc Natl Acad Sci U S A. 1987 Dec;84(23):8385-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/3479798 3479798]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Coll, M.]] | + | |
| - | [[Category: Frederick, C A.]] | + | |
| - | [[Category: Rich, A.]] | + | |
| - | [[Category: Wang, A H.J.]] | + | |
| - | [[Category: b-dna]]
| + | |
| - | [[Category: complexed with drug]]
| + | |
| - | [[Category: double helix]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:36:58 2008''
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