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RIGID BODY REFINEMENT OF WATER MEDIATED TRIPLE HELICAL STRUCTURE OF ß-D-1,3 XYLAN FROM PALMARIA PALMATA (L.) KUNTZE, RHODOPHYTA)

NAHEED AKHTAR, SADAF NAEEM, WASEEM AHMED* AND M.A. HALEEM**

Abstract: The triple helical structure of ß-D-1,3 xylan from the cell wall of Palmaria palmata (L.) Kuntze, (Rhodophyta) has been refined using the rigid body refinement technique. Water molecule is also included in the refinement. Using the least square rigid body refinement procedure the structure has been refined to an R-value of 0.338. The agreement between the calculated and observed structure factors is reasonably good. The results indicate that the sugar rings have limited freedom to rotate about 1, 3 glycosidic links and the molecule should be 9% smaller in radius. The position of water molecule is also refined. The loosely bound water follows the helical path. The present results support the view that inter and intra chain hydrogen bonds are possible in the water mediated structures.
 

Biophysics Unit, Department of Biochemistry, University of Karachi, Karachi, Pakistan.

Federal Urdu University, Karachi.
Sir Syed University of Engineering & Technology, Karachi.