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1d16

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[[Image:1d16.gif|left|200px]]
 
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==STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS==
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The line below this paragraph, containing "STRUCTURE_1d16", creates the "Structure Box" on the page.
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<StructureSection load='1d16' size='340' side='right'caption='[[1d16]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1d16]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1D16 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1d16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d16 OCA], [https://pdbe.org/1d16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1d16 RCSB], [https://www.ebi.ac.uk/pdbsum/1d16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1d16 ProSAT]</span></td></tr>
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{{STRUCTURE_1d16| PDB=1d16 | SCENE= }}
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</table>
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__TOC__
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'''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Chattopadhyaya R]]
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==Overview==
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[[Category: Dickerson RE]]
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The synthetic DNA oligomer C-G-C-G-C-G-T-T-T-T-C-G-C-G-C-G crystallizes as a Z-DNA hexamer, capped at one end by a T4 loop. The crystals are monoclinic, space group C2, with a = 57.18 A, b = 21.63 A, c = 36.40 A, beta = 95.22 degrees, and one hairpin molecule per asymmetric unit. The structure of the z-hexamer stem was determined by molecular replacement, and the T4 loop was positioned by difference map methods. The final R factor at 2.1 A resolution for hairpin plus 70 water molecules is 20% for 2 sigma data, with a root-mean-square error of 0.26 A. The (C-G)3 stem resembles the free Z-DNA hexamer with minor crystal packing effects. The T4 loop differs from that observed on a B-DNA stem in solution, or in longer loops in tRNA, in that it shows intraloop and intermolecular interactions rather than base stacking on the final base-pair of the stem. Bases T7, T8 and T9 stack with one another and with the sugar of T7. Two T10 bases from different molecules stack between the C1-G12 terminal base-pairs of a third and fourth molecule, to simulate a T.T "base-pair". Distances between thymine N and O atoms suggest that the two thymine bases are hydrogen bonded, and a keto-enol tautomer pair is favored over disordered keto-keto wobble pairs. The hairpin molecules pack in the crystal in herringbone columns in a manner that accounts well for the observed relative crystal growth rates in a, b and c directions. Hydration seems to be most extensive around the phosphate groups, with lesser hydration within the grooves.
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[[Category: Grzeskowiak K]]
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==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA].
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==Reference==
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Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops., Chattopadhyaya R, Grzeskowiak K, Dickerson RE, J Mol Biol. 1990 Jan 5;211(1):189-210. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/2299669 2299669]
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[[Category: Chattopadhyaya, R.]]
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[[Category: Dickerson, R E.]]
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[[Category: Grzeskowiak, K.]]
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[[Category: Hairpin loop]]
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[[Category: Single strand]]
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[[Category: Z-dna stem]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:20:01 2008''
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Current revision

STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS

PDB ID 1d16

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