The proper occupancy for an atom on a special position depends on how one defines the meaning of the number in that column. In the past, refinement programs, at least I know mine did, simply expanded all atoms in the coordinate file by the symmetry operators to determine the contents of the unit cell. With that operation the occupancy of the atoms on special positions had to be reduced. It is certainly true that there are 1/3 the number of atoms in the unit cell represented by "ZN D 31" than, for example, the CA of residue 50.
Most modern refinement programs try to handle this automatically, since users proved unreliable at detecting this condition and modifying their coordinate files. They use the interpretation that the "site" is fully occupied but there are only 1/3 the number of these "sites" than "sites" at general positions. Personally I find it disturbing to have the occupancy of "B 31" set to 0.33 and that of "D 31" set to 1.00 simply because of an insignificant shift in the position of the atom. Dale Tronrud On 12/10/10 13:53, Ian Tickle wrote: > Good point Colin! 2-Zn insulin is of course a classic example of > this, where the two independent Zn2+ ions both sit on the > crystallographic 3-fold in R3. It doesn't matter whether you count > the metal ion as part of the protein or not: if I understand Gloria's > original question correctly, all that matters is that the atom/ion is > present in the crystal structure. > > In fact here are some extracts from the PDB entry (4INS): > > REMARK 375 ZN ZN B 31 LIES ON A SPECIAL POSITION. > REMARK 375 ZN ZN D 31 LIES ON A SPECIAL POSITION. > REMARK 375 HOH B 251 LIES ON A SPECIAL POSITION. > REMARK 375 HOH D 44 LIES ON A SPECIAL POSITION. > REMARK 375 HOH D 134 LIES ON A SPECIAL POSITION. > REMARK 375 HOH D 215 LIES ON A SPECIAL POSITION. > REMARK 375 HOH D 269 LIES ON A SPECIAL POSITION. > > HETATM 835 ZN ZN B 31 -0.002 -0.004 7.891 0.33 10.40 ZN > HETATM 836 ZN ZN D 31 0.000 0.000 -8.039 0.33 11.00 ZN > HETATM 885 O HOH B 251 -0.023 -0.033 11.206 0.33 21.05 O > etc > > Hmmm - but shouldn't the occupancy of the Zn be 1.00 if it's on the > special position (assuming it's not disordered), though the first Zn > above and the water do appear to be disordered since they're not > actually on the special position. Fractional occupancy always implies > some kind of disorder: occupancy = 1/3 of an atom on a special > position would imply occupancy disorder, i.e. it's randomly present in > only 1/3 of the unit cells. > > -- Ian > > > On Fri, Dec 10, 2010 at 1:11 PM, Colin Nave <colin.n...@diamond.ac.uk> wrote: >> Does one regard the metal atom in a metalloprotein as being part of the >> protein? >> >> If so, a shared metal could occupy a special position in a dimer for example. >> >> In Acta Cryst. (2008). D64, 257-263 "Metals in proteins: correlation between >> the metal-ion type, coordination number and the amino-acid residues involved >> in the coordination" I. Dokmanic, M. Sikic and S. Tomic ( >> http://scripts.iucr.org/cgi-bin/paper?S090744490706595X ) it says there are >> 25 cases of metal atoms in special positions. >> >> Also Acta Cryst. (2002). D58, 29-38 "The 2.6 Å resolution structure of >> Rhodobacter capsulatus bacterioferritin with metal-free dinuclear site and >> heme iron in a crystallographic `special position' "D. Cobessi, L.-S. Huang, >> M. Ban, N. G. Pon, F. Daldal and E. A. Berry ( >> http://scripts.iucr.org/cgi-bin/paper?S0907444901017267 ) though the >> 'special position' is justifiably in quotation marks in this example as >> disorder is present. >> >> Colin >>
