362d
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 362d |SIZE=350|CAPTION= <scene name='initialview01'>362d</scene>, resolution 1.300Å | |PDB= 362d |SIZE=350|CAPTION= <scene name='initialview01'>362d</scene>, resolution 1.300Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</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=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=362d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=362d OCA], [http://www.ebi.ac.uk/pdbsum/362d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=362d RCSB]</span> | ||
}} | }} | ||
| Line 27: | Line 30: | ||
[[Category: Moore, M H.]] | [[Category: Moore, M H.]] | ||
[[Category: Schneider, B.]] | [[Category: Schneider, B.]] | ||
| - | [[Category: NCO]] | ||
[[Category: double helix]] | [[Category: double helix]] | ||
[[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 Mon Mar 31 05:21:47 2008'' |
Revision as of 02:21, 31 March 2008
| |||||||
| , resolution 1.300Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
THE STRUCTURE OF D(TGCGCA)2 AND A COMPARISON TO OTHER Z-DNA HEXAMERS
Overview
The X-ray crystal structure of d(TGCGCA)2 has been determined at 120 K to a resolution of 1.3 A. Hexamer duplexes, in the Z-DNA conformation, pack in an arrangement similar to the 'pure spermine form' [Egli et al. (1991). Biochemistry, 30, 11388-11402] but with significantly different cell dimensions. The phosphate backbone exists in two equally populated discrete conformations at one nucleotide step, around phosphate 11. The structure contains two ordered cobalt hexammine molecules which have roles in stabilization of both the Z-DNA conformation of the duplex and in crystal packing. A comparison of d(TGCGCA)2 with other Z-DNA hexamer structures available in the Nucleic Acid Database illustrates the elusive nature of crystal packing. A review of the interactions with the metal cations Na+, Mg2+ and Co3+ reveals a relatively small proportion of phosphate binding and that close contacts between metal ions are common. A prediction of the water structure is compared with the observed pattern in the reported structure.
About this Structure
362D is a Protein complex structure of sequences from [1]. This structure supersedes the now removed PDB entry 347D. Full crystallographic information is available from OCA.
Reference
Structure of d(TGCGCA)2 and a comparison to other DNA hexamers., Harper A, Brannigan JA, Buck M, Hewitt L, Lewis RJ, Moore MH, Schneider B, Acta Crystallogr D Biol Crystallogr. 1998 Nov 1;54(Pt 6 Pt 2):1273-84. PMID:10089504
Page seeded by OCA on Mon Mar 31 05:21:47 2008
