118d
From Proteopedia
| Line 4: | Line 4: | ||
|PDB= 118d |SIZE=350|CAPTION= <scene name='initialview01'>118d</scene>, resolution 1.640Å | |PDB= 118d |SIZE=350|CAPTION= <scene name='initialview01'>118d</scene>, resolution 1.640Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=118d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=118d OCA], [http://www.ebi.ac.uk/pdbsum/118d PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=118d RCSB]</span> | ||
}} | }} | ||
| Line 28: | Line 31: | ||
[[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 18:27:02 2008'' |
Revision as of 15:27, 30 March 2008
| |||||||
| , resolution 1.640Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL AND MOLECULAR STRUCTURE OF D(GTGCGCAC): INVESTIGATION OF THE EFFECTS OF BASE SEQUENCE ON THE CONFORMATION OF OCTAMER DUPLEXES
Overview
The structure of the self-complementary deoxyoctanucleotide d(GTGCGCAC), which crystallized as an A-type helix in the space group P4(3)2(1)2, with one strand in the crystallographic asymmetric unit has been determined and refined to a final R-value of 0.154 using 1.64-A diffraction data collected on an area detector. In contrast to the closely related sequence d(GTGTACAC)tet, there was no evidence for an ordered spermine molecule in the major groove of this octamer. Ordered water is found associated with almost all the exposed hydrogen bonding groups of the octamer. A pentagonal ring of water molecules is hydrogen bonded to O6 and N7 of G3 and the N4 and O6 of the C4.G13 base pair. A detailed comparison of the local helical parameters of d(GTGCGCAC) and d(GTGTACAC)tet is presented. The base sequence change at the center of the octamers affects several of the local helical parameters, via both intra- and interduplex interactions within the crystal.
About this Structure
118D is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Crystal and molecular structure of d(GTGCGCAC): investigation of the effects of base sequence on the conformation of octamer duplexes., Bingman C, Li X, Zon G, Sundaralingam M, Biochemistry. 1992 Dec 29;31(51):12803-12. PMID:1463751
Page seeded by OCA on Sun Mar 30 18:27:02 2008
