I doubt that you can tell the difference between Mg and water just from the
height of the density, but Mg2+ is always octahedrally coordinated with Mg-O
bond lengths ~2.0A At 2.9A resolution you may not be able to distinguish
Phil
On 14 Dec 2011, at 22:45, bie gao wrote:
Hi every,
I'm
Dear amit sir
you can go through this server ..
http://pic.mbu.iisc.ernet.in http://pic.mbu.iisc.ernet.in/index.html .
PIC server can calculate many interactions within and between the protein
molecules. ..PIC: Protein Interactions Calculator K. G.
LIGPLOT will show this graphically, if the correct parameters are set in
ligplot.prm, but not state the interactions explicitly:
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
The relevant lines in ligplot.prm:
PLOT PARAMETERS
---
Y- Include: Hydrophobic interactions - (Y/N)?
At 2A I think you will see the difference between the 2A bond Mg-GLU and
the likely 2.8A HOH-GLU.
Look at your difference map - put a peak there and check distances to
surrounding atoms.
Marjorie Hardings metal protein server gives a guide to other putative
Mg binding.
Eleanor
On
Post-Doctoral Position in Singapore: Chromatin Structure-Activity and
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projects at the cutting edge of structural biology and medicinal biochemistry
On 14/12/11 23:14, Jacob Keller wrote:
is there a convention for denoting/measuring pore sizes in protein
structures? Maybe inter-atom distances minus van der Waals radii?
AFAIK, the standard method is HOLE (Smart, Goodfellow, Wallace, 1993
(for example)).
The method has been implemented
Replying to my own post :-( ...
I forgot to mention that I wrote a GUI for it:
http://lmb.bioch.ox.ac.uk/coot/extras/test-hole.scm
Screeny here:
http://lmb.bioch.ox.ac.uk/coot/screenshots/Screenshot-Coot-hole.png
Dear Users,
The deadline for Feb/April 2012 Collaborative
Crystallography proposals will be *Dec 16, 2011. *
Through the Collaborative Crystallography Program (CC) at the
Advanced Light Source
Thank you all for the help. These are the key factors I collected so far:
1. Distance, Mg--O is shorter (2.0 -- 2.4A)
2. Coordination, Mg is octahedrally coordinated.
3. B factors, local B factors (i.e. the residues that coordinate with the
ion) should be similar.
4. Use Mn++ to replace Mg.
I will
