5vbj: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older editNewer edit →
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,330,058 edits
No edit summary
Line 3: Line 3:
<StructureSection load='5vbj' size='340' side='right'caption='[[5vbj]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
<StructureSection load='5vbj' size='340' side='right'caption='[[5vbj]], [[Resolution|resolution]] 1.94&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[5vbj]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5VBJ FirstGlance]. <br>
<table><tr><td colspan='2'>[[5vbj]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5VBJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5VBJ FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 1.944&#8491;</td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AS:2-DEOXY-ADENOSINE+-5-THIO-MONOPHOSPHATE'>AS</scene>, <scene name='pdbligand=BRU:5-BROMO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>BRU</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></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=5vbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbj OCA], [http://pdbe.org/5vbj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5vbj RCSB], [http://www.ebi.ac.uk/pdbsum/5vbj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbj ProSAT]</span></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=5vbj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5vbj OCA], [https://pdbe.org/5vbj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5vbj RCSB], [https://www.ebi.ac.uk/pdbsum/5vbj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5vbj ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br...S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single-crystal structure of the junction shows the geometry of the Br...S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to or slightly more stable than the analogous O acceptor, with a -3.5 kcal/mol difference in DeltaDeltaH(25( degrees )C) and -0.4 kcal/mol DeltaDeltaG(25( degrees )C) (including an entropic penalty DeltaDeltaS(25( degrees )C) of -10 cal/(mol K)). Thus sulfur is shown to be a favorable acceptor for bromine X-bonds, extending the application of this interaction for the design of inhibitors and biological materials.
Sulfur as an Acceptor to Bromine in Biomolecular Halogen Bonds.,Ford MC, Saxton M, Ho PS J Phys Chem Lett. 2017 Sep 7;8(17):4246-4252. doi: 10.1021/acs.jpclett.7b01725., Epub 2017 Aug 24. PMID:28796521<ref>PMID:28796521</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5vbj" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Ford, M C]]
[[Category: Synthetic construct]]
[[Category: Ho, P S]]
[[Category: Ford MC]]
[[Category: Biophysic]]
[[Category: Ho PS]]
[[Category: Bromine]]
[[Category: Dna]]
[[Category: Halogen bonding]]
[[Category: Model]]
[[Category: Molecular]]
[[Category: Molecular conformation]]
[[Category: Sulfur]]
[[Category: Uracil]]
Retrieved from "https://proteopedia.org/5vbj"