[phenixbb] Fucose alpha linkage

[Nigel Moriarty]

Tim

The glycosidic bonds in PHENIX are taken from the Monomer Lib so I
think that should be OK.

O1 can be in the axial or equatorial position depending on the ring
pucker but the O1 should always be on the opposite side of the ring
(if you imagine the ring is flattened) from the C6. It is the
chirality around the C1 atom that specifies the alpha/beta linkage.
Please send me the PDB file (off-line) so I can double-check that it
is correct. Just the three carbohydrate residues would be fine.

Cheers

Nigel

On Tue, Nov 29, 2011 at 3:13 PM, Timothy Springer
<springer at idi.harvard.edu> wrote:
> Hi, I have just added alpha1-3 and alpha1-6 fucoses to NAG. The Fucose in
> the monomer library has O1 in the alpha position, which is axial. However,
> after refinement, the fucose moves so it is linked beta in the equatorial
> position.  I believe the alpha and beta linkages for Fucose may be reversed
> in Phenix.  Please advise.
> The links are below.
>
>
>
>
>
>    apply_cif_link {
>      data_link = "ALPHA1-3"
>      residue_selection_1 = "chain A and resname NAG and resid 3821"
>      residue_selection_2 = "chain A and resname FUC and resid 3824"
>    }
>    apply_cif_link {
>      data_link = "ALPHA1-6"
>      residue_selection_1 = "chain A and resname NAG and resid 3821"
>      residue_selection_2 = "chain A and resname FUC and resid 3823"
>    }
>
>
> With my best regards,
> Tim
> Timothy A. Springer, Ph.D.
> Latham Family Professor of Biological Chemistry and Molecular Pharmacology
>
> Harvard Medical School                   http://idi.harvard.edu/springer
> Immune Disease Institute                 springer at idi.harvard.edu
> Program in Cellular and Molecular Medicine, Dept. Medicine
> Div. Hematology                                 Children's Hospital Boston
> 3 Blackfan Circle, Rm 3103              phone:  617-713-8200
> Boston MA 02115                               fax:        617-713-8232
>
>
>
>
>
>
>
>
>
>
>
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>



-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov