[phenixbb] on the protonation state of HIS

[Jeff Headd]

Hi Dialing,

Determining the protonation state of a HIS residue based on the diffraction
data would require very high resolution data (below 1.0A), if that is
possible at all.

However, it is possible to determine the protonation state of HIS residues
based on the local hydrogen-bonding network for a model at any resolution,
assuming it is well built. The program Reduce, which is the program used in
Phenix to add hydrogens to a model, does this automatically. Reduce looks
at the local hydrogen-bonding network created by neighboring residues and
other capable groups (waters, ligands, etc.) and then optimizes the HIS
orientation and protonation state. The three possibilities are delta
protonated (HD2), epsilon protonated (HE2), or both (HD2 and HE2).

You can read more about Reduce here:

http://kinemage.biochem.duke.edu/software/reduce.php

Jeff

On Fri, Apr 6, 2012 at 4:18 AM, Dialing Pretty <hdc123hdc123 at yahoo.com>wrote:

> Dear All,
>
> There may be PDB files which shows different protonation  state of HIS, at
> least there is PDB file shows double protonated HIS. At which resolution of
> the crystal can allow us to distinguish different protonation states of
> HIS?
>
> How do Phenix and Coot give different protonation states of HIS?
>
> I am looking forward to getting your reply.
>
> Cheers,
>
> Dialing
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120406/12352e5f/attachment.htm>