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Sodium in PDB 5ftu: Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2

Protein crystallography data

The structure of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2, PDB code: 5ftu 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) 206.73 / 6.00
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 292.360, 292.360, 291.770, 90.00, 90.00, 90.00
R / Rfree (%) 27.57 / 27.79

Other elements in 5ftu:

The structure of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 also contains other interesting chemical elements:

Calcium (Ca) 6 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 (pdb code 5ftu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2, PDB code: 5ftu:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 1 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1466

b:0.8
occ:1.00
 OD2 C:ASP436 2.2 0.7 1.0
OD1 C:ASP436 2.2 0.5 1.0
CG C:ASP436 2.5 0.2 1.0
OD1 C:ASP332 3.4 1.0 1.0
O C:PHE279 3.5 0.8 1.0
N C:PHE279 3.6 0.6 1.0
CA C:GLY278 3.6 0.7 1.0
CA C:CA1467 3.6 1.0 1.0
O C:LEU333 3.6 0.6 1.0
O C:THR277 3.7 0.7 1.0
C C:GLY278 3.9 0.6 1.0
CG C:ASP332 3.9 0.1 1.0
OD2 C:ASP332 4.0 0.5 1.0
CB C:ASP436 4.0 0.4 1.0
N C:LEU333 4.1 0.9 1.0
C C:PHE279 4.2 0.6 1.0
C C:LEU333 4.4 0.8 1.0
CA C:PHE279 4.5 0.2 1.0
N C:GLY278 4.5 0.6 1.0
C C:THR277 4.6 0.1 1.0
O C:VAL435 4.7 0.1 1.0
CA C:LEU333 4.7 0.0 1.0
CB C:ALA434 4.9 0.3 1.0
O C:GLY278 4.9 0.5 1.0
CA C:ASP436 5.0 0.7 1.0

Sodium binding site 2 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 2 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1465

b:1.0
occ:1.00
 O D:LEU333 2.3 0.9 1.0
O D:PHE279 2.5 0.2 1.0
OD1 D:ASP436 2.6 0.3 1.0
C D:PHE279 3.1 0.6 1.0
CG D:ASP436 3.2 0.9 1.0
N D:PHE279 3.2 0.2 1.0
C D:LEU333 3.4 0.0 1.0
OD2 D:ASP436 3.4 0.5 1.0
C D:GLY278 3.4 0.9 1.0
CB D:VAL280 3.7 0.1 1.0
N D:LEU333 3.7 0.3 1.0
CG2 D:VAL280 3.7 0.1 1.0
CA D:PHE279 3.8 0.4 1.0
CA D:GLY278 3.8 0.1 1.0
N D:VAL280 3.8 0.0 1.0
CA D:LEU333 3.8 1.0 1.0
O D:GLY278 3.9 0.3 1.0
CB D:LEU333 3.9 0.2 1.0
OD1 D:ASP332 4.0 0.8 1.0
CA D:VAL280 4.1 0.8 1.0
CB D:ASP436 4.5 0.1 1.0
CG D:ASP332 4.5 0.1 1.0
N D:ALA334 4.6 0.8 1.0
O D:THR277 4.7 0.8 1.0
OD2 D:ASP332 4.7 0.3 1.0
C D:ASP332 4.9 0.9 1.0
CG1 D:VAL280 4.9 1.0 1.0
CB D:PHE279 5.0 0.1 1.0
N D:GLY278 5.0 0.1 1.0

Sodium binding site 3 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 3 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1466

b:0.8
occ:1.00
 OD2 G:ASP436 2.2 0.7 1.0
OD1 G:ASP436 2.3 0.5 1.0
CG G:ASP436 2.6 0.2 1.0
OD1 G:ASP332 3.0 1.0 1.0
O G:THR277 3.3 0.7 1.0
CA G:CA1467 3.4 1.0 1.0
CA G:GLY278 3.5 0.7 1.0
O G:PHE279 3.5 0.8 1.0
O G:LEU333 3.6 0.6 1.0
C G:GLY278 3.7 0.6 1.0
N G:PHE279 3.8 0.6 1.0
CG G:ASP332 3.9 0.1 1.0
CB G:ASP436 4.1 0.4 1.0
C G:THR277 4.2 0.1 1.0
OD2 G:ASP332 4.2 0.5 1.0
N G:GLY278 4.3 0.6 1.0
C G:PHE279 4.3 0.6 1.0
O G:GLY278 4.4 0.5 1.0
N G:LEU333 4.6 0.9 1.0
O G:VAL435 4.6 0.1 1.0
CB G:ALA434 4.6 0.3 1.0
C G:LEU333 4.7 0.8 1.0
CA G:PHE279 4.7 0.2 1.0
CA G:ASP436 5.0 0.7 1.0
C G:VAL435 5.0 0.7 1.0

Sodium binding site 4 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 4 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1465

b:1.0
occ:1.00
 O H:LEU333 2.3 0.9 1.0
O H:PHE279 2.5 0.2 1.0
OD1 H:ASP436 2.6 0.3 1.0
C H:PHE279 3.1 0.6 1.0
CG H:ASP436 3.2 0.9 1.0
C H:LEU333 3.3 0.0 1.0
N H:PHE279 3.3 0.2 1.0
OD2 H:ASP436 3.4 0.5 1.0
C H:GLY278 3.5 0.9 1.0
CB H:VAL280 3.6 0.1 1.0
CG2 H:VAL280 3.7 0.1 1.0
N H:LEU333 3.7 0.3 1.0
CA H:LEU333 3.8 1.0 1.0
CA H:PHE279 3.8 0.4 1.0
N H:VAL280 3.8 0.0 1.0
CA H:GLY278 3.9 0.1 1.0
CB H:LEU333 3.9 0.2 1.0
O H:GLY278 4.0 0.3 1.0
OD1 H:ASP332 4.1 0.8 1.0
CA H:VAL280 4.1 0.8 1.0
CB H:ASP436 4.5 0.1 1.0
N H:ALA334 4.5 0.8 1.0
CG H:ASP332 4.6 0.1 1.0
O H:THR277 4.8 0.8 1.0
OD2 H:ASP332 4.8 0.3 1.0
C H:ASP332 4.8 0.9 1.0
CG1 H:VAL280 4.9 1.0 1.0
CA H:ALA334 5.0 0.9 1.0

Sodium binding site 5 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 5 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Na1466

b:0.8
occ:1.00
 OD2 K:ASP436 2.2 0.7 1.0
OD1 K:ASP436 2.3 0.5 1.0
CG K:ASP436 2.6 0.2 1.0
OD1 K:ASP332 3.0 1.0 1.0
CA K:GLY278 3.3 0.7 1.0
O K:THR277 3.3 0.7 1.0
O K:PHE279 3.5 0.8 1.0
O K:LEU333 3.5 0.6 1.0
C K:GLY278 3.6 0.6 1.0
N K:PHE279 3.8 0.6 1.0
CG K:ASP332 3.9 0.1 1.0
CA K:CA1467 3.9 1.0 1.0
CB K:ASP436 4.1 0.4 1.0
C K:THR277 4.2 0.1 1.0
N K:GLY278 4.2 0.6 1.0
OD2 K:ASP332 4.3 0.5 1.0
O K:GLY278 4.3 0.5 1.0
C K:PHE279 4.3 0.6 1.0
N K:LEU333 4.5 0.9 1.0
C K:LEU333 4.6 0.8 1.0
O K:VAL435 4.6 0.1 1.0
CA K:PHE279 4.7 0.2 1.0
CB K:ALA434 4.7 0.3 1.0

Sodium binding site 6 out of 6 in 5ftu

Go back to Sodium Binding Sites List in 5ftu
Sodium binding site 6 out of 6 in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2 within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Na1465

b:1.0
occ:1.00
 O L:LEU333 2.3 0.9 1.0
OD1 L:ASP436 2.5 0.3 1.0
O L:PHE279 2.6 0.2 1.0
C L:PHE279 3.1 0.6 1.0
CG L:ASP436 3.2 0.9 1.0
N L:PHE279 3.3 0.2 1.0
C L:LEU333 3.4 0.0 1.0
C L:GLY278 3.4 0.9 1.0
OD2 L:ASP436 3.4 0.5 1.0
N L:LEU333 3.6 0.3 1.0
CA L:GLY278 3.7 0.1 1.0
CB L:VAL280 3.7 0.1 1.0
CA L:PHE279 3.8 0.4 1.0
CA L:LEU333 3.8 1.0 1.0
CG2 L:VAL280 3.8 0.1 1.0
O L:GLY278 3.9 0.3 1.0
N L:VAL280 3.9 0.0 1.0
OD1 L:ASP332 3.9 0.8 1.0
CB L:LEU333 3.9 0.2 1.0
CA L:VAL280 4.3 0.8 1.0
CG L:ASP332 4.4 0.1 1.0
CB L:ASP436 4.5 0.1 1.0
N L:ALA334 4.5 0.8 1.0
OD2 L:ASP332 4.6 0.3 1.0
O L:THR277 4.6 0.8 1.0
C L:ASP332 4.8 0.9 1.0
CA L:CA1466 4.9 0.8 1.0
N L:GLY278 4.9 0.1 1.0
CG1 L:VAL280 5.0 1.0 1.0

Reference:

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
Page generated: Tue Dec 15 11:00:00 2020

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