Sodium in PDB 3bib: Tim-4 in Complex with Phosphatidylserine

The structure of Tim-4 in Complex with Phosphatidylserine, PDB code: 3bib was solved by C.Santiago, A.Ballesteros, G.G.Kaplan, G.J.Freeman, J.M.Casasnovas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.50
Space group	P 63 2 2
Cell size a, b, c (Å), α, β, γ (°)	66.260, 66.260, 139.390, 90.00, 90.00, 120.00
R / Rfree (%)	21.9 / 24.8

The binding sites of Sodium atom in the Tim-4 in Complex with Phosphatidylserine (pdb code 3bib). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Tim-4 in Complex with Phosphatidylserine, PDB code: 3bib:

Sodium binding site 1 out of 1 in the Tim-4 in Complex with Phosphatidylserine


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tim-4 in Complex with Phosphatidylserine within 5.0Å range: probe atom residue distance (Å) B Occ X:Na117 b:34.3 occ:1.00 O4 X:PSF118 2.2 41.8 1.0 OD1 X:ASN99 2.3 41.1 1.0 O X:VAL94 2.4 36.7 1.0 O X:GLY96 2.6 40.8 1.0 OD1 X:ASP100 2.7 36.7 1.0 O X:HOH165 2.9 43.0 1.0 P X:PSF118 3.4 41.2 1.0 CG X:ASN99 3.6 40.2 1.0 C X:GLY96 3.6 40.7 1.0 C X:VAL94 3.6 36.6 1.0 O1 X:PSF118 3.8 40.8 1.0 CG X:ASP100 3.8 37.8 1.0 N X:ASN99 3.9 40.7 1.0 N X:ASP100 3.9 38.9 1.0 CB X:PSF118 4.0 40.3 1.0 O3 X:PSF118 4.2 40.0 1.0 N X:VAL94 4.2 35.7 1.0 N X:PHE98 4.3 41.6 1.0 N X:TRP97 4.3 41.7 1.0 N X:GLY96 4.3 39.1 1.0 ND2 X:ASN99 4.3 39.9 1.0 C X:ASN99 4.3 39.7 1.0 CA X:TRP97 4.3 42.1 1.0 C X:PRO95 4.4 38.4 1.0 CA X:VAL94 4.4 36.2 1.0 CA X:ASN99 4.4 40.1 1.0 C X:TRP97 4.4 42.2 1.0 CA X:GLY96 4.5 40.0 1.0 OD2 X:ASP100 4.5 37.6 1.0 CA X:ASP100 4.6 38.1 1.0 CB X:ASN99 4.6 40.1 1.0 CB X:VAL94 4.6 36.3 1.0 N X:PRO95 4.7 37.1 1.0 CB X:ASP100 4.7 37.9 1.0 O X:PRO95 4.7 38.5 1.0 O2 X:PSF118 4.7 42.9 1.0 CA X:PRO95 4.7 37.7 1.0 N X:PSF118 4.9 40.1 1.0 C X:PHE98 4.9 41.4 1.0

C.Santiago, A.Ballesteros, L.Martinez-Munoz, M.Mellado, G.G.Kaplan, G.J.Freeman, J.M.Casasnovas. Structures of T Cell Immunoglobulin Mucin Protein 4 Show A Metal-Ion-Dependent Ligand Binding Site Where Phosphatidylserine Binds. Immunity V. 27 941 2007.
ISSN: ISSN 1074-7613
PubMed: 18083575
DOI: 10.1016/J.IMMUNI.2007.11.008