Sodium in PDB 5ftt: Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr)

The structure of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr), PDB code: 5ftt was solved by V.A.Jackson, S.Mehmood, M.Chavent, P.Roversi, M.Carrasquero, D.Del Toro, G.Seyit-Bremer, F.M.Ranaivoson, D.Comoletti, M.S.P.Sansom, C.V.Robinson, R.Klein, E.Seiradake, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	133.83 / 3.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	231.961, 141.486, 151.491, 90.00, 117.94, 90.00
R / Rfree (%)	22.52 / 24.46

The structure of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) (pdb code 5ftt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr), PDB code: 5ftt:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1466 b:0.8 occ:1.00 OD2 C:ASP436 2.5 0.7 1.0 OD1 C:ASP436 2.6 0.5 1.0 CG C:ASP436 2.8 0.2 1.0 O C:GLY278 3.0 0.5 1.0 O C:PHE279 3.1 0.8 1.0 C C:GLY278 3.2 0.6 1.0 O C:THR277 3.4 0.7 1.0 CA C:GLY278 3.4 0.7 1.0 OD1 C:ASP332 3.5 1.0 1.0 O C:LEU333 3.7 0.6 1.0 N C:PHE279 3.9 0.6 1.0 CA C:CA1467 4.0 1.0 1.0 C C:PHE279 4.1 0.6 1.0 C C:THR277 4.2 0.1 1.0 N C:GLY278 4.3 0.6 1.0 CB C:ASP436 4.4 0.4 1.0 CG C:ASP332 4.6 0.1 1.0 CA C:PHE279 4.6 0.2 1.0 N C:LEU333 4.7 0.9 1.0 C C:LEU333 4.8 0.8 1.0

Sodium binding site 2 out of 4 in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na1465 b:1.0 occ:1.00 O D:PHE279 2.6 0.2 1.0 OD1 D:ASP436 2.8 0.3 1.0 O D:LEU333 2.9 0.9 1.0 C D:GLY278 3.0 0.9 1.0 OD2 D:ASP436 3.1 0.5 1.0 N D:PHE279 3.1 0.2 1.0 C D:PHE279 3.1 0.6 1.0 CG D:ASP436 3.3 0.9 1.0 CA D:GLY278 3.4 0.1 1.0 O D:GLY278 3.5 0.3 1.0 OD1 D:ASP332 3.6 0.8 1.0 CA D:PHE279 3.7 0.4 1.0 C D:LEU333 3.9 0.0 1.0 CG2 D:VAL280 3.9 0.1 1.0 N D:VAL280 3.9 0.0 1.0 CB D:VAL280 3.9 0.1 1.0 N D:LEU333 4.0 0.3 1.0 O D:THR277 4.2 0.8 1.0 CA D:LEU333 4.3 1.0 1.0 CB D:LEU333 4.3 0.2 1.0 CA D:VAL280 4.3 0.8 1.0 CG D:ASP332 4.5 0.1 1.0 N D:GLY278 4.6 0.1 1.0 CB D:ASP436 4.7 0.1 1.0 C D:THR277 4.8 0.8 1.0 CB D:PHE279 4.9 0.1 1.0

Sodium binding site 3 out of 4 in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) within 5.0Å range: probe atom residue distance (Å) B Occ G:Na1466 b:1.0 occ:1.00 OD2 G:ASP436 3.0 0.4 1.0 OD1 G:ASP332 3.1 0.0 1.0 N G:PHE279 3.1 0.5 1.0 CA G:GLY278 3.1 0.8 1.0 O G:THR277 3.2 0.9 1.0 OD1 G:ASP436 3.4 0.2 1.0 O G:PHE279 3.4 0.9 1.0 CG G:ASP436 3.5 0.6 1.0 C G:GLY278 3.6 0.3 1.0 C G:THR277 3.6 0.6 1.0 N G:GLY278 3.6 0.3 1.0 CG G:ASP332 4.2 0.6 1.0 C G:PHE279 4.2 0.1 1.0 CA G:PHE279 4.2 0.1 1.0 O G:LEU333 4.3 0.3 1.0 CA G:CA1467 4.4 0.9 1.0 CB G:ALA434 4.4 0.8 1.0 CB G:ALA225 4.5 0.4 1.0 OD2 G:ASP332 4.8 0.5 1.0 OG1 G:THR277 4.8 0.4 1.0 N G:LEU333 4.8 0.7 1.0 O G:GLY278 4.9 0.5 1.0 CA G:THR277 4.9 1.0 1.0 CB G:THR277 4.9 0.8 1.0

Sodium binding site 4 out of 4 in the Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Octameric Complex of Latrophilin 3 (Lec, Olf) , UNC5D (Ig, IG2, TSP1) and FLRT2 (Lrr) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1463 b:0.0 occ:1.00 O H:PHE279 2.3 0.1 1.0 C H:GLY278 2.7 0.1 1.0 O H:GLY278 2.7 0.4 1.0 O H:LEU333 2.9 0.7 1.0 C H:PHE279 3.0 0.8 1.0 N H:PHE279 3.1 0.5 1.0 CA H:GLY278 3.3 0.4 1.0 OD1 H:ASP436 3.4 0.2 1.0 N H:LEU333 3.6 0.4 1.0 CA H:PHE279 3.6 0.0 1.0 OD2 H:ASP436 3.7 0.3 1.0 C H:LEU333 3.8 0.8 1.0 O H:THR277 3.8 0.8 1.0 CG H:ASP436 4.0 0.3 1.0 CA H:LEU333 4.0 0.3 1.0 N H:VAL280 4.0 0.5 1.0 CB H:LEU333 4.0 0.7 1.0 CB H:VAL280 4.0 0.5 1.0 OD2 H:ASP332 4.2 0.2 1.0 CG2 H:VAL280 4.2 0.7 1.0 N H:GLY278 4.3 0.2 1.0 CA H:VAL280 4.4 0.6 1.0 C H:THR277 4.5 0.3 1.0 CG H:ASP332 4.5 0.3 1.0 C H:ASP332 4.7 0.5 1.0 CB H:PHE279 4.7 0.8 1.0 OD1 H:ASP332 4.8 0.6 1.0 CA H:ASP332 4.9 1.0 1.0

V.A.Jackson, S.Mehmood, M.Chavent, P.Roversi, M.Carrasquero, D.Del Toro, G.Seyit-Bremer, F.M.Ranaivoson, D.Comoletti, M.S.P.Sansom, C.V.Robinson, R.Klein, E.Seiradake. Super-Complexes of Adhesion Gpcrs and Neural Guidance Receptors Nat.Commun. V. 7 11184 2016.
ISSN: ISSN 2041-1723
PubMed: 27091502
DOI: 10.1038/NCOMMS11184