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

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

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

Sodium

(Na)

6 atoms

The binding sites of Calcium 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 Calcium atom.
In total 6 binding sites of Calcium where determined in the Tetrameric Complex of Latrophilin 3, UNC5D and FLRT2, PDB code: 5ftu:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium 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 Calcium with other atoms in the Ca 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:Ca1467 b:1.0 occ:1.00 O C:VAL435 2.1 0.1 1.0 OD2 C:ASP332 2.1 0.5 1.0 O C:ALA381 2.7 0.1 1.0 OD1 C:ASP436 2.7 0.5 1.0 CG C:ASP332 3.0 0.1 1.0 OD1 C:ASP332 3.1 1.0 1.0 C C:VAL435 3.2 0.7 1.0 CG C:ASP436 3.3 0.2 1.0 OD1 C:ASN380 3.5 0.9 1.0 NA C:NA1466 3.6 0.8 1.0 CA C:ASP436 3.8 0.7 1.0 OD2 C:ASP436 3.9 0.7 1.0 C C:ALA381 3.9 0.6 1.0 N C:ASP436 3.9 0.9 1.0 CB C:ASP436 4.1 0.4 1.0 CB C:ASP332 4.4 0.0 1.0 CA C:VAL435 4.4 0.7 1.0 N C:VAL435 4.4 0.7 1.0 CA C:PHE382 4.5 0.7 1.0 CB C:PHE382 4.6 0.7 1.0 N C:PHE382 4.6 0.7 1.0 CG C:ASN380 4.7 0.2 1.0 O C:LEU333 4.7 0.6 1.0 CB C:ALA334 4.8 0.0 1.0 CD1 C:ILE343 4.8 0.5 1.0 N C:ALA381 4.9 0.0 1.0 CA C:ALA381 5.0 0.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1466 b:0.8 occ:1.00 O D:VAL435 2.3 0.8 1.0 OD2 D:ASP332 2.5 0.3 1.0 OD1 D:ASP332 2.8 0.8 1.0 O D:ALA381 2.8 0.8 1.0 OD1 D:ASN380 2.9 0.8 1.0 CG D:ASP332 2.9 0.1 1.0 C D:VAL435 3.4 0.5 1.0 N D:VAL435 3.7 0.1 1.0 OD1 D:ASP436 3.8 0.3 1.0 C D:ALA381 3.9 0.5 1.0 CA D:VAL435 4.1 0.6 1.0 CG D:ASN380 4.1 0.7 1.0 N D:ALA381 4.1 0.9 1.0 CG D:ASP436 4.2 0.9 1.0 CB D:ASP332 4.3 0.6 1.0 OD2 D:ASP436 4.3 0.5 1.0 N D:ASP436 4.4 0.2 1.0 OH D:TYR323 4.5 0.2 1.0 CA D:ALA381 4.6 0.1 1.0 CB D:VAL435 4.7 0.2 1.0 CB D:ASN380 4.7 0.6 1.0 CA D:ASP436 4.7 0.8 1.0 C D:ALA434 4.8 0.5 1.0 CA D:ALA434 4.9 0.5 1.0 N D:PHE382 5.0 0.8 1.0 CB D:ALA434 5.0 0.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1467 b:1.0 occ:1.00 OD2 G:ASP332 2.3 0.5 1.0 O G:VAL435 2.3 0.1 1.0 OD1 G:ASP332 2.5 1.0 1.0 CG G:ASP332 2.7 0.1 1.0 OD1 G:ASN380 2.8 0.9 1.0 O G:ALA381 3.0 0.1 1.0 OD1 G:ASP436 3.2 0.5 1.0 C G:VAL435 3.4 0.7 1.0 NA G:NA1466 3.4 0.8 1.0 CG G:ASP436 3.7 0.2 1.0 CG G:ASN380 3.9 0.2 1.0 N G:VAL435 4.0 0.7 1.0 OD2 G:ASP436 4.0 0.7 1.0 C G:ALA381 4.2 0.6 1.0 CB G:ASP332 4.2 0.0 1.0 CA G:VAL435 4.3 0.7 1.0 N G:ASP436 4.3 0.9 1.0 ND2 G:ASN380 4.4 0.6 1.0 CA G:ASP436 4.4 0.7 1.0 O G:LEU333 4.5 0.6 1.0 N G:ALA381 4.6 0.0 1.0 CB G:ASP436 4.7 0.4 1.0 CB G:VAL435 4.9 0.4 1.0 OH G:TYR323 5.0 0.2 1.0 CA G:ALA381 5.0 0.5 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1466 b:0.8 occ:1.00 O H:VAL435 2.3 0.8 1.0 OD2 H:ASP332 2.5 0.3 1.0 OD1 H:ASP332 2.8 0.8 1.0 O H:ALA381 2.9 0.8 1.0 OD1 H:ASN380 2.9 0.8 1.0 CG H:ASP332 2.9 0.1 1.0 C H:VAL435 3.3 0.5 1.0 OD1 H:ASP436 3.7 0.3 1.0 N H:VAL435 3.7 0.1 1.0 C H:ALA381 4.0 0.5 1.0 CA H:VAL435 4.0 0.6 1.0 CG H:ASN380 4.1 0.7 1.0 CG H:ASP436 4.1 0.9 1.0 N H:ALA381 4.2 0.9 1.0 OD2 H:ASP436 4.3 0.5 1.0 CB H:ASP332 4.3 0.6 1.0 N H:ASP436 4.4 0.2 1.0 OH H:TYR323 4.5 0.2 1.0 CB H:VAL435 4.6 0.2 1.0 CA H:ALA381 4.7 0.1 1.0 CA H:ASP436 4.7 0.8 1.0 CB H:ASN380 4.7 0.6 1.0 C H:ALA434 4.7 0.5 1.0 CA H:ALA434 4.9 0.5 1.0 CB H:ALA434 5.0 0.0 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1467 b:1.0 occ:1.00 OD2 K:ASP332 2.2 0.5 1.0 O K:VAL435 2.2 0.1 1.0 O K:ALA381 2.5 0.1 1.0 CG K:ASP332 2.9 0.1 1.0 OD1 K:ASP332 2.9 1.0 1.0 OD1 K:ASP436 3.0 0.5 1.0 OD1 K:ASN380 3.1 0.9 1.0 C K:VAL435 3.4 0.7 1.0 C K:ALA381 3.7 0.6 1.0 CG K:ASP436 3.8 0.2 1.0 NA K:NA1466 3.9 0.8 1.0 CA K:ASP436 4.2 0.7 1.0 N K:ASP436 4.2 0.9 1.0 CG K:ASN380 4.3 0.2 1.0 O K:LEU333 4.3 0.6 1.0 OD2 K:ASP436 4.4 0.7 1.0 N K:VAL435 4.4 0.7 1.0 CB K:ASP332 4.4 0.0 1.0 CA K:VAL435 4.4 0.7 1.0 N K:ALA381 4.5 0.0 1.0 N K:PHE382 4.5 0.7 1.0 CA K:PHE382 4.5 0.7 1.0 CB K:ASP436 4.6 0.4 1.0 CD1 K:ILE343 4.6 0.5 1.0 CA K:ALA381 4.6 0.5 1.0 CB K:PHE382 4.7 0.7 1.0 CB K:ALA334 4.9 0.0 1.0 CB K:VAL435 5.0 0.4 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca1466 b:0.8 occ:1.00 OD2 L:ASP332 2.4 0.3 1.0 O L:VAL435 2.4 0.8 1.0 OD1 L:ASP332 2.6 0.8 1.0 CG L:ASP332 2.8 0.1 1.0 OD1 L:ASN380 2.9 0.8 1.0 O L:ALA381 3.0 0.8 1.0 C L:VAL435 3.5 0.5 1.0 OD1 L:ASP436 3.6 0.3 1.0 N L:VAL435 3.7 0.1 1.0 CG L:ASP436 4.1 0.9 1.0 CG L:ASN380 4.1 0.7 1.0 CA L:VAL435 4.2 0.6 1.0 CB L:ASP332 4.2 0.6 1.0 C L:ALA381 4.2 0.5 1.0 OD2 L:ASP436 4.2 0.5 1.0 N L:ALA381 4.3 0.9 1.0 N L:ASP436 4.5 0.2 1.0 OH L:TYR323 4.5 0.2 1.0 C L:ALA434 4.7 0.5 1.0 CA L:ASP436 4.8 0.8 1.0 CB L:ASN380 4.8 0.6 1.0 CB L:VAL435 4.8 0.2 1.0 CA L:ALA381 4.8 0.1 1.0 CA L:ALA434 4.8 0.5 1.0 CB L:ALA434 4.9 0.0 1.0 NA L:NA1465 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