Hi Mish,
At physiological pH the carboxylate group will have a negative charge which
will be shared between the two oxygens. It is common to represent the
structure as (COOH) with all the valencies filled but in solution that
proton will come off. Again it is common to represent that as O=C-O with a
negative charge on the right hand side oxygen but really that charge is
shared between the two oxygens. It's called resonance hybridization. The
double bond you see is probably put there by whatever visualizer/builder you
are using.
Oliver
On 28 July 2011 10:29, mish <smncbr.gmail.com> wrote:
> Hi all:
>
> My question is related to preparing the structure of 3' Sialyllactose using
> GLYCAM. In databse (http://www.hmdb.ca/metabolites/HMDB00825) I can see
> that
> this structure is nothing but tri-saccharides linked in fallowing way.
> A-D-Neu5Ac-(2-3)-B-D-Galp-(1-4)-B-D-Glcp-(1-1)-OH
> I modeled the structure in GLYCAM web interface but I can see a difference
> in the structure of Neu5Ac (0SA) residue. C1 of 0SA has two oxygens O1A
> and
> O1B making double bond with C1. This makes the sugar charged. Whereas if we
> look for the structure published in article or in the same data base its
> just a -COOH group. Can you please correct me if I am going in wrong
> direction or whats is the possible way to overcome ? Replacing O1A or O1B
> with ROH should be fine or I have to be careful about something else ?
>
> Sincerely
> Mish
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Received on Thu Jul 28 2011 - 03:00:06 PDT
