192d
From Proteopedia
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|PDB= 192d |SIZE=350|CAPTION= <scene name='initialview01'>192d</scene>, resolution 1.920Å | |PDB= 192d |SIZE=350|CAPTION= <scene name='initialview01'>192d</scene>, resolution 1.920Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NA:SODIUM ION'>NA</scene> | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=192d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=192d OCA], [http://www.ebi.ac.uk/pdbsum/192d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=192d RCSB]</span> | ||
}} | }} | ||
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[[Category: Subirana, J A.]] | [[Category: Subirana, J A.]] | ||
[[Category: Urpi, L.]] | [[Category: Urpi, L.]] | ||
| - | [[Category: NA]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[Category: flipped-out base]] | [[Category: flipped-out base]] | ||
[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''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 18:29:51 2008'' |
Revision as of 15:29, 30 March 2008
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| , resolution 1.920Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
RECOMBINATION-LIKE STRUCTURE OF D(CCGCGG)
Overview
We have solved the single crystal X-ray structure of the synthetic DNA hexamer d(CCGCGG). The central alternating tetramer forms a Z-DNA duplex. The initial cytosine of each strand of the duplex swings out and forms a Watson-Crick base-pair with the terminal guanine of a symmetry-related molecule. Thus, two symmetry-related DNA molecules form a twin with intermolecular base-pairs at both ends. Such a twin is additionally stabilized by a sodium ion located on a dyad axis between two DNA duplexes. The total structure has recombination-like features. It also provides a model for B/Z junctions. The crystal used in this study belongs to space group C222(1) with a = 34.33 A, b = 44.04 A and c = 38.27 A. The structure was solved by molecular replacement using partial models, and refined by molecular dynamics simulated annealing and positional treatment. The refinement has been concluded with an R-factor of 18.5% for 2377 reflections with F > or = 2 sigma (F) in the resolution region 8.0 to 1.92 A. The asymmetric unit contains two strands of d(CCGCGG) and 38 water molecules.
About this Structure
192D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Recombination-like structure of d(CCGCGG)., Malinina L, Urpi L, Salas X, Huynh-Dinh T, Subirana JA, J Mol Biol. 1994 Oct 28;243(3):484-93. PMID:7966274
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