PDBsum entry 1qrk

Go to PDB code: 
Top Page protein metals Protein-protein interface(s) links
Transferase PDB id
Protein chain
700 a.a. *
_SR ×2
Waters ×230
* Residue conservation analysis

References listed in PDB file
Key reference
Title Identification of the calcium binding site and a novel ytterbium site in blood coagulation factor xiii by x-Ray crystallography.
Authors B.A.Fox, V.C.Yee, L.C.Pedersen, I.Le trong, P.D.Bishop, R.E.Stenkamp, D.C.Teller.
Ref. J Biol Chem, 1999, 274, 4917-4923. [DOI no: 10.1074/jbc.274.8.4917]
PubMed id 9988734
The presence or absence of calcium determines the activation, activity, oligomerization, and stability of blood coagulation factor XIII. To explore these observed effects, we have determined the x-ray crystal structure of recombinant factor XIII A2 in the presence of calcium, strontium, and ytterbium. The main calcium binding site within each monomer involves the main chain oxygen atom of Ala-457, and also the side chains from residues Asn-436, Asp-438, Glu-485, and Glu-490. Calcium and strontium bind in the same location, while ytterbium binds several angstroms removed. A novel ytterbium binding site is also found at the dimer two-fold axis, near residues Asp-270 and Glu-272, and this site may be related to the reported inhibition by lanthanide metals (Achyuthan, K. E., Mary, A., and Greenberg, C. S. (1989) Biochem. J. 257, 331-338). The overall structure of ion-bound factor XIII is very similar to the previously determined crystal structures of factor XIII zymogen, likely due to the constraints of this monoclinic crystal form. We have merged the three independent sets of water molecules in the structures to determine which water molecules are conserved and possibly structurally significant.
Figure 1.
Fig. 1. Overall structure of the factor XIII dimer. Panel A is the dimer looking down the two-fold axis. The domains, activation peptide (AP), and N and C termini of one monomer are labeled. Panel B shows one monomer, rotated 90° with the domains, N terminus, active site (AS), and ion sites labeled. For both views, three unique spheres are also shown: novel ytterbium site on the dimer two-fold axis (medium gray), active site (light gray), and main ion site (dark gray).
Figure 6.
Fig. 6. Structurally significant water molecule. Water 6059S is shown as a sphere with several secondary structure elements nearby. The residues near this water are also shown. The active site residue His-373 and calcium binding ligand Ala-457 are shown.
The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 4917-4923) copyright 1999.
Go to PROCHECK summary