Dear Jiamu, The density is definitely carbohydrate. The N-links are highly conserved so build N-acetylglucosamine (NAG) beta 1-Asn. Both the C2 acetyl group and the C6 group lie outside the ring so look for the diagonal bulge in your density to assign the orientation. To sanity check your torsion angles you may with to consult Petrescu et al. A statistical analysis of N- and O-glycan linkage conformations from crystallographic data. Glycobiology. 1999 Apr;9(4):343-52 and http://www.dkfz.de/spec/glycosciences.de/tools/pdbcare/.
>From your picture, you may be unable to build the next beta 1-4 NAG. As you >are using the CHO system, if you see additional denistity off the C6 (which I >don't think you do) this is likely to be alpha 1-6 fucose. If you are careful to position the NAG, refmac should detect the linkages. Best of luck! Max Crispin ================================================ Dr Max Crispin The Division of Structural Biology The Henry Wellcome Building for Genomic Medicine University of Oxford Roosevelt Drive Headington Oxford, OX3 7BN Lab: 01865 287551 Mob: 07889 932694 College address: Dr Max Crispin Lecturer in Biochemistry Oriel College Oxford OX1 4EW ================================================
