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1d16

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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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Retrieved from "http://52.214.119.220/wiki/index.php/1d16"

Categories: Large Structures | Chattopadhyaya R | Dickerson RE | Grzeskowiak K

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-[[Image:1d16.gif|left|200px]]<br /><applet load="1d16" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1d16, resolution 2.100&Aring;" />
-'''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''<br />
-==Overview==
+==STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS==
-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.
+<StructureSection load='1d16' size='340' side='right'caption='[[1d16]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<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>
-D16 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA].
+</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>
+<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>
-==Reference==
+</table>
-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://ispc.weizmann.ac.il//pmbin/getpm?pmid=2299669 2299669]
+__TOC__
-[[Category: Protein complex]]
+</StructureSection>
-[[Category: Chattopadhyaya, R.]]
+[[Category: Large Structures]]
-[[Category: Dickerson, R.E.]]
+[[Category: Chattopadhyaya R]]
-[[Category: Grzeskowiak, K.]]
+[[Category: Dickerson RE]]
-[[Category: hairpin loop]]
+[[Category: Grzeskowiak K]]
-[[Category: single strand]]
-[[Category: z-dna stem]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:13:46 2007''

1d16

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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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