Dear coot users:
I in order to solve my protein structure via experimental phasing, I
soaked my crystals in potassium tetracyanoplatinate (II) hydrate. In my
(almost) final model I could identify two binding sites where two
metionines are coordinating (I guess) a platinum ion. The two heavy atom
sites had high occupancy (I did the phasing using sharp). I still can
not find a way to improve the geometry, bond length and coordinates of
the sites. Moreover, when I calculate the clashing score using REDUCE
and PROBE, the programs indicate a horrible cluster of clashes in the
vicinity of the platinum sites. I placed the platinum using the tool:
add atom at pointer in coot (the platinum ion option was not present in
the selection window, therefore I typed "PT". Coot always tells me in
the terminal the following message:
Debug:: there were 2 types with no dictionary
PT
PT
I also was checking how were defined the LINK records in PDB files
with platinum bound; however, I did not manage to place it properly in
my model (in order to refine them). Obviously I am doing something wrong.
Here are the questions:
Do you know a proper way [for dummies :-) ] of placing a platinum or
heavy metal atom in a final model?
Do you know how do the platinum sites have to be defined in the PDB file?
Do you know which is the best way to generate a .cif file or dictionary
in order to refine the platinum sites?
Thanks in advance for your time, wish you a nice day!
All the best
Jose Arcadio Farias Rico
PhD Student
Höcker Group (Protein Design)
http://www.eb.tuebingen.mpg.de/research-groups/birte-hocker/protein-design
MPI for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
Tel: +49 7071 601 365
Fax: +49 7071 601 305
E-Mail: [email protected]
