AMBER Archive (2009)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Jun 15 2009 - 11:39:04 CDT

Hi,

Edit the residue name in the pdb. If it is HIS I 'think' it defaults to epsilon. The residue names to use are:

HID = delta protonated
HIE = epsilon protonated
HIP = doubly protonated (+1 charge)

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of s. Bill
> Sent: Monday, June 15, 2009 9:28 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Histidine, which form?
>
> 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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