1bdn
From Proteopedia
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|PDB= 1bdn |SIZE=350|CAPTION= <scene name='initialview01'>1bdn</scene>, resolution 2.600Å | |PDB= 1bdn |SIZE=350|CAPTION= <scene name='initialview01'>1bdn</scene>, resolution 2.600Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM ION'>MG</scene> | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bdn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bdn OCA], [http://www.ebi.ac.uk/pdbsum/1bdn PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1bdn RCSB]</span> | ||
}} | }} | ||
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[[Category: Sanderson, M R.]] | [[Category: Sanderson, M R.]] | ||
[[Category: Steitz, T A.]] | [[Category: Steitz, T A.]] | ||
| - | [[Category: MG]] | ||
[[Category: b-dna]] | [[Category: b-dna]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
| - | ''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 18:58:53 2008'' |
Revision as of 15:58, 30 March 2008
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| , resolution 2.600Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL LATTICE PACKING IS IMPORTANT IN DETERMINING THE BEND OF A DNA DODECAMER CONTAINING AN ADENINE TRACT
Overview
The crystal structure of a DNA duplex dodecamer d(CGCAAAAATGCG) and its complementary strand has been determined at 2.6-A resolution. Although our goal was to deduce the structural features of the static bending of the helical axis exhibited by adenine-tract structures in solution, we conclude that the overall bend of 20 degrees in the direction of the major groove observed here arises from the forces associated with crystal packing. An isomorphous dodecamer brominated on one strand provides experimental evidence that this asymmetric sequence is positioned in two orientations in the crystal lattice that are related by a 180 degrees rotation around the pseudodyad axis of the sequence. The bend in these two differently positioned DNA molecules depends on their orientation in the crystal, not on their sequence. As with previously determined structures containing adenine tracts, the adenine and thymine base pairs are highly propeller twisted. The N-6 of the adenine comes within hydrogen bonding distance of the O-4 of thymine one step down the helix, facilitating the formation of a series of bifurcated hydrogen bonds within the adenine tract. The adenine tract is relatively straight and the bending is localized outside this region.
About this Structure
1BDN is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract., DiGabriele AD, Sanderson MR, Steitz TA, Proc Natl Acad Sci U S A. 1989 Mar;86(6):1816-20. PMID:2928304
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