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 >
