You can look for similar loops in other structures in the PDB using the Protein Geometry Database (http://pgd.science.oregonstate.edu/). The search page allows you to specify phi/psi ranges for loops up to ten amino acids long and the "Browse Results" page will list out the ID codes and residues of any matches found.
If you need any detailed assistance using this server, I'd be happy to help. Dale Tronrud On 07/02/10 05:44, Domen Zafred wrote: > Dear all, > > There is an odd loop on the surface of my structure. Three back-bone > oxygen atoms are turned in the same direction the structure is > stabilized by an cation and water molecules. > Also, the ion is probably partly occupied (as discussed in the recent > post of Ivan Xaravich). The pictures in crossed-eye stereo are in the > attachment. Electron densities are at 1.8 and 3.5 sigma. > I have two problems regarding this loop: > > Is such a loop something known or common, or is it unique? How could I > find structure with a similar feature? > > Is there a smart guess for finding out the right ion? Mg is the smallest > of all and there is still some red density. Ca on the other hand is more > common in cells and the puzzle is whether it is a small ion or is it > bigger, but with lover occupancy. > > Any suggestions, comments or answers will be greatly appreciated. > > Regards, > > Domen Zafred
