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1ixj
From Proteopedia
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|PDB= 1ixj |SIZE=350|CAPTION= <scene name='initialview01'>1ixj</scene>, resolution 2.5Å | |PDB= 1ixj |SIZE=350|CAPTION= <scene name='initialview01'>1ixj</scene>, resolution 2.5Å | ||
|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>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ixj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixj OCA], [http://www.ebi.ac.uk/pdbsum/1ixj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ixj RCSB]</span> | ||
}} | }} | ||
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[[Category: Takenaka, A.]] | [[Category: Takenaka, A.]] | ||
[[Category: Watanabe, K.]] | [[Category: Watanabe, K.]] | ||
| - | [[Category: MG]] | ||
| - | [[Category: NCO]] | ||
[[Category: homo base pair]] | [[Category: homo base pair]] | ||
[[Category: parallel dna]] | [[Category: parallel dna]] | ||
| Line 35: | Line 36: | ||
[[Category: parallel-stranded helix]] | [[Category: parallel-stranded 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 21:26:08 2008'' |
Revision as of 18:26, 30 March 2008
| |||||||
| , resolution 2.5Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs
Overview
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half of the oligomer form a parallel duplex with another half through the homo base pairs, C2:C2+ (singly-protonated between the Watson- Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The two strands remaining in the half of the parallel duplex are split away in different directions, and they pair in an anti-parallel B-form duplex with the second half extending from a neighboring parallel duplex, so that an infinite column is formed in a head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt cation supports such a branched and bent conformation of the oligomer. One end of the parallel duplex is stacked on the corresponding end of the adjacent parallel duplex; between them, the guanine base of the first residue is stacked on the fourth ribose of another duplex.
About this Structure
1IXJ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs., Sunami T, Kondo J, Kobuna T, Hirao I, Watanabe K, Miura K, Takenaka A, Nucleic Acids Res. 2002 Dec 1;30(23):5253-60. PMID:12466550
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