It was not my intent to get involved in a debate like this. I sent a
back-channel note to point out that if you are unfamiliar with alpha and
beta in sugar bonds, are thinking D sugar, and you actually have an L
sugar, you might confuse in a structure whether you have an alpha or beta
linkage. Typically, when using opposite and same we are thinking of
Haworth projections. Alpha is opposite in a Haworth projection (or anti,
thus easy to remember), and the same side in a Fischer (which complicates
things, is less intuitively interpretable as a structure, and makes this
harder to remember). Perhaps I should have given an in depth description
and I'm sure my description could have been much better. I wrote the note
quickly in the hopes of helping someone.
Draw out Fischer projections for all four forms of glucose, convert them
to Haworth diagrams and you have alpha D with axial constituents on C5 and
C1, with C6 above the ring, the C1 hydroxyl below. With alpha L, again,
two axial constituents, but this time C6 below and the C1 hydroxyl above
the ring. With beta-D, two axial constituents, both above the ring, with
beta-L, two axial constituents, both below the ring. Hope this helps,
Kelvin Luther
ps. If you want to show a picture of the sugar model, perhaps we could
determine if it really is alpha or beta.
On Thu, 14 Jun 2007, Kim Henrick wrote:
perhaps there still is a problem with refmac
from the iupac carbohydrate pages
http://www.chem.qmul.ac.uk/iupac/2carb/06n07.html
see section 2-Carb-7.4. Enantiomers
if a sugar has a configuration in a chair form for
a trans 1--6 then it will be trans-like in both alpha-L and alpha-D
1C4 to 4C1 but both are axial -O1
see the example above url
á-D-glucopyranose-4C1 and á-L-glucopyranose-1C4
the 1,2-torsion changes stays cis or trans depending
on the actual sugar
changing a 1,6, a five bond connectivity is not possible
the orientations stay the same
in plane project for alpha-fucose
L has O1 O2 up O3 O4 C5 down
D has O1 O2 down O3 O4 C5 up
no change in any cis or trans torsions
in the PDB
a-D-FUC is 3-letter code FCA
a-L-FUC is 3-letter code FUC
you can get the ideal coordinates fro FUC and FCA from either the
http://www.ebi.ac.uk/msd-srv/msdchem/
or the wwpdb
http://remediation.wwpdb.org/downloads.html
and the dictionaries from G.K.
http://alpha2.bmc.uu.se/hicup/
alpha and beta change torsion angles from cis/trans
Sorry guys,
my previous message obviously reflected that I am not very familiar with
sugars. Kelvin's email clarified what was going on: the REFMAC dictionary
for a-L-fucose is perfectly correct, my mistake was that I was not aware
of the reverse relation of alpha and beta-linkages in L and D-sugars!
Thanks again for the clarification, and sorry for bugging you all,
the sugar-greenhorn Petra
---------------------------- Original Message ----------------------------
Subject: Re: [ccp4bb] REFMAC converts alpha-L-fucose into beta-L-fucose
From: "Kelvin Luther" <[EMAIL PROTECTED]>
Date: Wed, June 13, 2007 5:00 pm
To: [EMAIL PROTECTED]
--------------------------------------------------------------------------
I just wanted to mention something in case you're not familiar with
sugars. Alpha and Beta for an L sugar will be reverse of alpha and beta
for a D sugar. Alpha for a D-sugar is when the c6 constituent and the
anomeric carbon constituent are in opposite orientations. With fucose,
an L sugar, such a configuration would be beta. Hope this is the
problem, in which case, there isn't one.
Cheers,this
Kelvin Luther
