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| - | [[Image:1d16.gif|left|200px]] | |
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| - | {{Structure
| + | ==STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS== |
| - | |PDB= 1d16 |SIZE=350|CAPTION= <scene name='initialview01'>1d16</scene>, resolution 2.100Å
| + | <StructureSection load='1d16' size='340' side='right'caption='[[1d16]], [[Resolution|resolution]] 2.10Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=
| + | __TOC__ |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1d16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1d16 OCA], [http://www.ebi.ac.uk/pdbsum/1d16 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1d16 RCSB]</span>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Chattopadhyaya R]] |
| - | '''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS'''
| + | [[Category: Dickerson RE]] |
| - | | + | [[Category: Grzeskowiak K]] |
| - | | + | |
| - | ==Overview==
| + | |
| - | 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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| - | ==About this Structure==
| + | |
| - | 1D16 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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: Protein complex]] | + | |
| - | [[Category: Chattopadhyaya, R.]] | + | |
| - | [[Category: Dickerson, R E.]] | + | |
| - | [[Category: Grzeskowiak, K.]] | + | |
| - | [[Category: hairpin loop]]
| + | |
| - | [[Category: single strand]]
| + | |
| - | [[Category: z-dna stem]]
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| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:32:27 2008''
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