On 20/07/2019 18:33, Ahmad Khalifa wrote:
After generating metal ion restraints using Elbow in Phenix and refining my structure, I end up with a
structure that forms two solid bonds between the GTP and Mg+2.
You will get solid bond if the GTP and Mg+2 are in the same residue (I'd recommend that you don't do that)
or are in consecutive residues and are sufficiently close.
Comparing my model to two structures in the pdb (3jar and 5syf), they show dashed line bonds in Coot (see
screenshot), and 5syf appears to have an extra bond with a glutamate that is absent in both my model and 3jar.
Dotted lines represent LINK records. If you have links and consecutive residues, then you will have both -
but it will be hard to see the dots.
It's quite possible that the GLU has undergone radiation damage and for the most part of the data collection
is no longer in a position to make bonds to the Mg+2 with both of its Oxygen atoms.
According to this resource here, the Mg+2 should forms octahedral coordinate
bonds:
http://www.cryst.bbk.ac.uk/PPS2/projects/vun/p21Hras_master.htm
Quite right.
Although the following was mentioned, in the structure that they reference (5p21), there appears to be two
more extra bonds with two waters:
"Mg++ forms octahedral coordinate bonds. When GTP is bound, two neighbouring equatorial dative bonds are
connected to 2 oxygen atoms of the beta and gamma phosphates of GTP, whilst the other two equatorial bonds
are connected to the hydroxyl oxygen of Ser17 and Thr35, respectively. Both polar dative bonds are linked to
water molecules"
The bonds to waters complete the octahedron.
Does coot work out these bonds based on distance or does it come from
information in the coordinate file?
Both. Atoms are bonded by dictionary if its a ligand, by distance for everything else and then the LINK
records are added.
What is the correct way to model the bonds of GTP and Mg+2 with tubulin?! (not really Coot related, but I
would appreciate some input regarding that).
I am not sure why the GTP and Mg+2 in tubulin should be different to other proteins. Make 6 LINK records to
the Mg+2 (if you can model your waters) and (for aesthetic reasons) leave a residue number gap between the
GTP and Mg+2.
Paul.
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