231d: Difference between revisions

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{{Seed}}
[[Image:231d.png|left|200px]]


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==STRUCTURE OF A DNA-PORPHYRIN COMPLEX==
The line below this paragraph, containing "STRUCTURE_231d", creates the "Structure Box" on the page.
<StructureSection load='231d' size='340' side='right'caption='[[231d]], [[Resolution|resolution]] 2.40&Aring;' 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'>[[231d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=231D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=231D 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]] 2.4&#8491;</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=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PCU:CU(II)MESO(4-N-TETRAMETHYLPYRIDYL)PORPHYRIN'>PCU</scene></td></tr>
{{STRUCTURE_231d|  PDB=231d  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=231d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=231d OCA], [https://pdbe.org/231d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=231d RCSB], [https://www.ebi.ac.uk/pdbsum/231d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=231d ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
We report the 2.4 A resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack. The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin], and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack. The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs. Two pyridyl rings are located in each groove of the DNA. The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex. Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes.


===STRUCTURE OF A DNA-PORPHYRIN COMPLEX===
Structure of DNA-porphyrin complex.,Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:8608116<ref>PMID:8608116</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 231d" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 8608116 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_8608116}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=231D OCA].
[[Category: Lipscomb LA]]
 
[[Category: Peek ME]]
==Reference==
[[Category: Plaskon RR]]
Structure of DNA-porphyrin complex., Lipscomb LA, Zhou FX, Presnell SR, Woo RJ, Peek ME, Plaskon RR, Williams LD, Biochemistry. 1996 Mar 5;35(9):2818-23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8608116 8608116]
[[Category: Presnell SR]]
[[Category: Lipscomb, L A.]]
[[Category: Williams LD]]
[[Category: Peek, M E.]]
[[Category: Woo RJ]]
[[Category: Plaskon, R R.]]
[[Category: Zhou FX]]
[[Category: Presnell, S R.]]
[[Category: Williams, L D.]]
[[Category: Woo, R J.]]
[[Category: Zhou, F X.]]
[[Category: Complexed with drug]]
[[Category: Double helix]]
[[Category: Flipped-out base]]
[[Category: Right handed dna]]
 
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