1d16: Difference between revisions
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|PDB= 1d16 |SIZE=350|CAPTION= <scene name='initialview01'>1d16</scene>, resolution 2.100Å | |PDB= 1d16 |SIZE=350|CAPTION= <scene name='initialview01'>1d16</scene>, resolution 2.100Å | ||
|SITE= | |SITE= | ||
|LIGAND= | |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> | ||
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
|DOMAIN= | |||
|RELATEDENTRY= | |||
|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> | |||
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[[Category: z-dna stem]] | [[Category: z-dna stem]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 19:32:27 2008'' | ||
Revision as of 19:32, 30 March 2008
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| , resolution 2.100Å | |||||||
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| Ligands: | , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
OverviewOverview
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.
About this StructureAbout this Structure
1D16 is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
ReferenceReference
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:2299669
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