Calcium in PDB 3kaa: Structure of Tim-3 in Complex with Phosphatidylserine

The structure of Structure of Tim-3 in Complex with Phosphatidylserine, PDB code: 3kaa was solved by A.Ballesteros, C.Santiago, J.M.Casasnovas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.93 / 3.00
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	71.922, 71.922, 263.579, 90.00, 90.00, 120.00
R / Rfree (%)	23.5 / 24.5

The binding sites of Calcium atom in the Structure of Tim-3 in Complex with Phosphatidylserine (pdb code 3kaa). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was determined in the Structure of Tim-3 in Complex with Phosphatidylserine, PDB code: 3kaa:

Calcium binding site 1 out of 1 in the Structure of Tim-3 in Complex with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Tim-3 in Complex with Phosphatidylserine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca119 b:92.7 occ:1.00 O B:PHE96 2.6 66.3 1.0 O B:GLY98 2.7 80.8 1.0 O4 B:PSF120 2.9 78.3 1.0 OD2 B:ASP102 3.0 0.4 1.0 CB B:PSF120 3.1 0.1 1.0 OD1 B:ASN101 3.1 78.8 1.0 C B:GLY98 3.6 75.1 1.0 C B:PHE96 3.8 65.8 1.0 CG B:ASP102 3.8 97.9 1.0 OD1 B:ASP102 3.9 97.7 1.0 O1 B:PSF120 3.9 0.3 1.0 P B:PSF120 4.0 71.9 1.0 CG B:ASN101 4.1 73.4 1.0 CA B:LEU99 4.2 77.4 1.0 CA B:PSF120 4.2 0.9 1.0 N B:LEU99 4.3 73.1 1.0 N B:GLY98 4.3 72.0 1.0 C B:PRO97 4.3 71.3 1.0 ND2 B:ASN101 4.4 63.7 1.0 N B:PHE96 4.5 74.5 1.0 CA B:PRO97 4.6 69.6 1.0 CA B:GLY98 4.6 72.9 1.0 N B:PRO97 4.6 66.0 1.0 CA B:PHE96 4.7 67.9 1.0 O B:PRO97 4.8 68.8 1.0 N B:MET100 4.8 73.9 1.0 CD1 B:LEU99 4.8 87.7 1.0 O3 B:PSF120 4.8 61.9 1.0 C B:LEU99 4.8 80.4 1.0 N B:PSF120 4.8 0.6 1.0 C B:GLN95 4.8 79.2 1.0

R.H.Dekruyff, X.Bu, A.Ballesteros, C.Santiago, Y.L.Chim, H.H.Lee, P.Karisola, M.Pichavant, G.G.Kaplan, D.T.Umetsu, G.J.Freeman, J.M.Casasnovas. T Cell/Transmembrane, Ig, and Mucin-3 Allelic Variants Differentially Recognize Phosphatidylserine and Mediate Phagocytosis of Apoptotic Cells. J.Immunol. V. 184 1918 2010.
ISSN: ISSN 0022-1767
PubMed: 20083673
DOI: 10.4049/JIMMUNOL.0903059