414d
From Proteopedia
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|PDB= 414d |SIZE=350|CAPTION= <scene name='initialview01'>414d</scene>, resolution 1.900Å | |PDB= 414d |SIZE=350|CAPTION= <scene name='initialview01'>414d</scene>, resolution 1.900Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=414d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=414d OCA], [http://www.ebi.ac.uk/pdbsum/414d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=414d RCSB]</span> | ||
}} | }} | ||
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[[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 Mon Mar 31 05:36:58 2008'' |
Revision as of 02:37, 31 March 2008
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| , resolution 1.900Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
5'-D(*GP*GP*GP*GP*CP*GP*CP*CP*CP*C)-3'
Overview
The crystal and molecular structure of the self-complementary A-DNA decamer sequence d(G4CGC4) was solved at 1.9 A resolution. The decamer crystallizes in space group P21 with two independent duplexes in the asymmetric unit. Duplex 1 has interactions which are distributed symmetrically about its length compared with duplex 2. The two end base pairs of duplex 1 have a similar NH.O hydrogen-bond pattern involving GGC segments of duplex 2 and a symmetry-related neighbour, while the end base pairs of duplex 2 interact with the GCC and GGG segments of its symmetry-related neighbours through NH.O and NH.N hydrogen bonds and a water-mediated hydrogen bond between the carboxyl groups of C40 and C8. In addition to the C4'-C5' torsion angle gamma assuming the trans conformation in certain steps, this angle also adopts the gauche- conformation at C37 as opposed to the preferred gauche+ conformation, with a concomitant change in phosphodiester P-O5' (alpha) in the opposite sense. This facilitates stacking between adjacent bases. The study suggests that the structural alterations in the two molecules in the asymmetric unit originate from an inherent propensity of the d(G4CGC4) base sequence for varied intermolecular interactions and malleability.
About this Structure
414D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
An A-DNA structure with two independent duplexes in the asymmetric unit., Savitha G, Viswamitra MA, Acta Crystallogr D Biol Crystallogr. 1999 Jun;55(Pt 6):1136-43. PMID:10329775
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