1d16
From Proteopedia
| Line 1: | Line 1: | ||
[[Image:1d16.gif|left|200px]] | [[Image:1d16.gif|left|200px]] | ||
| - | + | <!-- | |
| - | + | The line below this paragraph, containing "STRUCTURE_1d16", creates the "Structure Box" on the page. | |
| - | + | You may change the PDB parameter (which sets the PDB file loaded into the applet) | |
| - | + | or the SCENE parameter (which sets the initial scene displayed when the page is loaded), | |
| - | | | + | or leave the SCENE parameter empty for the default display. |
| - | | | + | --> |
| - | + | {{STRUCTURE_1d16| PDB=1d16 | SCENE= }} | |
| - | + | ||
| - | + | ||
| - | }} | + | |
'''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS''' | '''STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS''' | ||
| Line 19: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
| - | + | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D16 OCA]. | |
==Reference== | ==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] | 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] | ||
| - | [[Category: Protein complex]] | ||
[[Category: Chattopadhyaya, R.]] | [[Category: Chattopadhyaya, R.]] | ||
[[Category: Dickerson, R E.]] | [[Category: Dickerson, R E.]] | ||
[[Category: Grzeskowiak, K.]] | [[Category: Grzeskowiak, K.]] | ||
| - | [[Category: | + | [[Category: Hairpin loop]] |
| - | [[Category: | + | [[Category: Single strand]] |
| - | [[Category: | + | [[Category: Z-dna stem]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 13:20:01 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 10:20, 2 May 2008
STRUCTURE OF A T4 HAIRPIN LOOP ON A Z-DNA STEM AND COMPARISON WITH A-RNA AND B-DNA LOOPS
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.
About this Structure
Full crystallographic information is available from OCA.
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:2299669 Page seeded by OCA on Fri May 2 13:20:01 2008
