AMBER Archive (2006)

Subject: Re: AMBER: Zinc-coordinating histidine protonation state

From: David A. Case (
Date: Mon Jul 31 2006 - 10:50:16 CDT

On Thu, Jul 27, 2006, Nitin Bhardwaj wrote:

> The zinc-coordinating Histidine in my NMR structure does not have
> any hydrogen (neither on delta nor on epsilon nitrogen) where as the
> other non-zinc-coordinating histidines have delta protonation (HID).
> So, I was wondering what is usually the protonation state of the
> histidines that coordinate zinc (HID or HIE)?

The usual protonation state is that the nitrogen not coordinated to the zinc
has a proton bonded to it.

> And also what is the default protonation state oh histidine in amber?
> If I say HIS, does amber take it as HIE or HID?

Default in Amber is HIE.


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