Sodium in PDB 5afb: Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains

The structure of Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains, PDB code: 5afb was solved by V.A.Jackson, D.Del Toro, M.Carrasquero, P.Roversi, K.Harlos, R.Klein, E.Seiradake, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.91 / 2.16
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	78.430, 96.650, 101.640, 90.00, 90.00, 90.00
R / Rfree (%)	20.44 / 24.52

The structure of Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Sodium atom in the Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains (pdb code 5afb). 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 Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains, PDB code: 5afb:

Sodium binding site 1 out of 1 in the Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of the LATROPHILIN3 Lectin and Olfactomedin Domains within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1460 b:39.4 occ:1.00 O A:HOH2058 2.2 31.9 1.0 OD1 A:ASP332 2.3 37.6 1.0 O A:LEU333 2.3 31.1 1.0 OD1 A:ASP436 2.6 39.3 1.0 O A:GLY278 2.7 33.2 1.0 C A:GLY278 3.2 34.0 1.0 O A:HOH2072 3.3 31.1 1.0 C A:LEU333 3.4 32.1 1.0 O A:PHE279 3.5 32.4 1.0 CG A:ASP332 3.5 37.8 1.0 O A:HOH2071 3.5 29.8 1.0 CA A:GLY278 3.6 31.3 1.0 N A:LEU333 3.6 31.5 1.0 CG A:ASP436 3.6 41.0 1.0 OD2 A:ASP436 3.9 47.8 1.0 CA A:LEU333 4.0 30.4 1.0 N A:PHE279 4.1 30.4 1.0 C A:PHE279 4.1 33.0 1.0 OD2 A:ASP332 4.1 40.8 1.0 CA A:CA1461 4.3 55.6 1.0 C A:ASP332 4.3 36.1 1.0 O A:THR277 4.4 35.5 1.0 CG2 A:VAL280 4.4 32.7 1.0 CB A:LEU333 4.5 30.7 1.0 N A:ALA334 4.5 28.3 1.0 CB A:ASP332 4.6 33.4 1.0 CA A:ASP332 4.6 31.7 1.0 CA A:PHE279 4.7 29.8 1.0 N A:GLY278 4.8 32.1 1.0 CA A:ALA334 4.9 27.9 1.0 O A:VAL435 4.9 38.4 1.0 CB A:VAL280 4.9 32.8 1.0 CB A:ASP436 4.9 34.5 1.0 N A:VAL280 4.9 29.5 1.0

V.A.Jackson, D.Del Toro, M.Carrasquero, P.Roversi, K.Harlos, R.Klein, E.Seiradake. Structural Basis of Latrophilin-Flrt Interaction. Structure 2015.
ISSN: ESSN 1878-4186
PubMed: 25728924
DOI: 10.1016/J.STR.2015.01.013