AMBER Archive (2009)

Subject: Re: [AMBER] Histidine, which form?

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Mon Jun 15 2009 - 11:28:27 CDT

Dear Dr. Carlos / Ross
Thanks so much for your interest.
As you know, Hydrogens atoms are added by Xleap, so how can I decide my histadine which one of the three types?
I checked my PDB file, I found my histidine is not bonded throughout imidazol ring. So, which form is it?
In other way, could you support me with three different examples, please?
Thanks in Advance

--- On Mon, 15/6/09, Carlos Simmerling <carlos.simmerling_at_gmail.com> wrote:

From: Carlos Simmerling <carlos.simmerling_at_gmail.com>
Subject: Re: [AMBER] Histidine, which form?
To: s_bill36_at_yahoo.co.uk, "AMBER Mailing List" <amber_at_ambermd.org>
Date: Monday, 15 June, 2009, 2:57 PM

the delta N is the one closer to the alpha carbon- atoms are labeled in
order alpha, beta, gamma, delta, epsilon moving out the side chain. not sure
what you mean by an example of HIP- this would be His at low pH. most x=-ay
crystal structures have no H atoms so it is not clear which of the 3 forms
it really is. you need other experiments to tell.

On Mon, Jun 15, 2009 at 10:54 AM, <s_bill36_at_yahoo.co.uk> wrote:

> Dear AMBER
> For Histidine, there are three forms of it, HIE, HID, and HIP.
> Delta poistion is position number 1 and Epsilon Position is position number
> 3.
> The problem is that:
> There two different systems of numbering the atoms in the
> imidazole ring of histidine had both been used for a considerable time
> (biochemists
> generally numbering as 1 the nitrogen atom adjacent to the side chain, and
> organic chemists
> designating it as 3).
>
> So, could you tell me which nitrogen atom is the delta one, please?
> Also, could you give me an example of HIP when histidine is protonated on
> both positions, please?
>
> Thanks in Advance
>
>
>
>
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