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

Protein crystallography data

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

Other elements in 5afb:

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

Calcium (Ca) 1 atom

Sodium Binding Sites:

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 5afb

Go back to Sodium Binding Sites List in 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

Reference:

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
Page generated: Tue Dec 15 10:20:04 2020

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