2h9s
From Proteopedia
(Difference between revisions)
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[2h9s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9S FirstGlance]. <br> | <table><tr><td colspan='2'>[[2h9s]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2H9S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2H9S FirstGlance]. <br> | ||
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XAD:9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE'>XAD</scene>, <scene name='pdbligand=XCT:4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE'>XCT</scene>, <scene name='pdbligand=XGU:2-AMINO-9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>XGU</scene>, <scene name='pdbligand=XTH:1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>XTH</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]] 1.75Å</td></tr> |
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=XAD:9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-9H-PURIN-6-AMINE'>XAD</scene>, <scene name='pdbligand=XCT:4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE'>XCT</scene>, <scene name='pdbligand=XGU:2-AMINO-9-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-1,9-DIHYDRO-6H-PURIN-6-ONE'>XGU</scene>, <scene name='pdbligand=XTH:1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE'>XTH</scene></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=2h9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9s OCA], [https://pdbe.org/2h9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9s RCSB], [https://www.ebi.ac.uk/pdbsum/2h9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9s 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=2h9s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2h9s OCA], [https://pdbe.org/2h9s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2h9s RCSB], [https://www.ebi.ac.uk/pdbsum/2h9s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2h9s ProSAT]</span></td></tr> | ||
</table> | </table> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | An experimental rationalization of the structure type encountered in DNA and RNA by systematically investigating the chemical and physical properties of alternative nucleic acids has identified systems with a variety of sugar-phosphate backbones that are capable of Watson-Crick base pairing and in some cases cross-pairing with the natural nucleic acids. The earliest among the model systems tested to date, (4' --> 6')-linked oligo(2',3'-dideoxy-beta-d-glucopyranosyl)nucleotides or homo-DNA, shows stable self-pairing, but the pairing rules for the four natural bases are not the same as those in DNA. However, a complete interpretation and understanding of the properties of the hexapyranosyl (4' --> 6') family of nucleic acids has been impeded until now by the lack of detailed 3D-structural data. We have determined the crystal structure of a homo-DNA octamer. It reveals a weakly twisted right-handed duplex with a strong inclination between the hexose-phosphate backbones and base-pair axes, and highly irregular values for helical rise and twist at individual base steps. The structure allows a rationalization of the inability of allo-, altro-, and glucopyranosyl-based oligonucleotides to form stable pairing systems. | ||
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| - | Crystal structure of homo-DNA and nature's choice of pentose over hexose in the genetic system.,Egli M, Pallan PS, Pattanayek R, Wilds CJ, Lubini P, Minasov G, Dobler M, Leumann CJ, Eschenmoser A J Am Chem Soc. 2006 Aug 23;128(33):10847-56. PMID:16910680<ref>PMID:16910680</ref> | ||
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| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
| - | </div> | ||
| - | <div class="pdbe-citations 2h9s" style="background-color:#fffaf0;"></div> | ||
| - | == References == | ||
| - | <references/> | ||
__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
Current revision
Crystal Structure of Homo-DNA and Nature's Choice of Pentose over Hexose in the Genetic System
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