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| | ==CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN== |
| The line below this paragraph, containing "STRUCTURE_261d", creates the "Structure Box" on the page.
| | <StructureSection load='261d' size='340' side='right'caption='[[261d]], [[Resolution|resolution]] 2.40Å' scene=''> |
| You may change the PDB parameter (which sets the PDB file loaded into the applet)
| | == Structural highlights == |
| or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| | <table><tr><td colspan='2'>[[261d]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=261D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=261D FirstGlance]. <br> |
| or leave the SCENE parameter empty for the default display.
| | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</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=NT:NETROPSIN'>NT</scene></td></tr> |
| {{STRUCTURE_261d| PDB=261d | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=261d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=261d OCA], [https://pdbe.org/261d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=261d RCSB], [https://www.ebi.ac.uk/pdbsum/261d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=261d ProSAT]</span></td></tr> |
| | | </table> |
| '''CRYSTAL STRUCTURE OF THE DNA DECAMER D(CGCAATTGCG) COMPLEXED WITH THE MINOR GROOVE BINDING DRUG NETROPSIN'''
| | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Garman E]] |
| The crystal structure of netropsin bound to the decamer d(CGCAATTGCG) has been determined at 2.4 A resolution. This is the first example of a crystal structure of netropsin bound to decamer DNA. The central eight bases of each DNA single-strand base pair with a self-complementary strand to form an octamer B-DNA duplex. These duplexes lie end to end within the unit cell. The terminal 5'-C and G-3' bases are unpaired and interact with the neighboring duplexes via interactions within both the major and minor groove to form base triplet interactions of the type C(+)-G x C and G*(G x C), respectively. The triplet interaction of the type C(+)-G x C is known to exist within triplex DNA with the C+ base oriented parallel with the Watson-Crick guanine base to which it hydrogen bonds. The netropsin molecule lies within the minor groove of the octamer duplex and assumes a class I type position, with bifurcated hydrogen-bonding interactions from the amide groups of the netropsin to the A x T base pairs of the minor groove. The netropsin molecule fits within a five base pair long minor groove site by bending of the flexible amidinium group at one end of the drug.
| | [[Category: Neidle S]] |
| | | [[Category: Nunn CM]] |
| ==About this Structure== | |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=261D OCA]. | |
| | |
| ==Reference== | |
| Crystal structure of the DNA decamer d(CGCAATTGCG) complexed with the minor groove binding drug netropsin., Nunn CM, Garman E, Neidle S, Biochemistry. 1997 Apr 22;36(16):4792-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9125500 9125500]
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| [[Category: Garman, E.]]
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| [[Category: Neidle, S.]]
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| [[Category: Nunn, C M.]]
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| [[Category: B-dna]]
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| [[Category: Complexed with drug]]
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| [[Category: Continuous helix]] | |
| [[Category: Double helix]] | |
| [[Category: Flipped-out base]] | |
| [[Category: Intermolecular base triplet]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 18:24:19 2008''
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