Calcium in PDB 5cmn: FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain

The structure of FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain, PDB code: 5cmn was solved by Y.Lu, G.Salzman, D.Arac, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	73.20 / 3.61
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	102.268, 102.268, 419.230, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 26.2

The binding sites of Calcium atom in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain (pdb code 5cmn). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain, PDB code: 5cmn:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ E:Ca401 b:0.1 occ:1.00 OD2 E:ASP264 2.4 0.7 1.0 OD1 E:ASP264 2.4 1.0 1.0 OD1 E:ASN312 2.4 96.3 1.0 O E:ALA313 2.4 0.4 1.0 O E:VAL367 2.4 0.2 1.0 CG E:ASP264 2.6 1.0 1.0 C E:VAL367 3.5 99.1 1.0 C E:ALA313 3.6 0.5 1.0 CG E:ASN312 3.6 96.5 1.0 N E:ALA313 3.9 0.1 1.0 OD1 E:ASP368 3.9 0.0 1.0 CB E:ASP264 4.0 0.6 1.0 N E:VAL367 4.2 0.6 1.0 CA E:ALA313 4.3 0.2 1.0 ND2 E:ASN312 4.3 90.2 1.0 CA E:VAL367 4.4 0.5 1.0 CG E:ASP368 4.4 0.0 1.0 N E:ASP368 4.5 96.9 1.0 O E:LEU265 4.5 0.4 1.0 N E:PHE314 4.6 0.8 1.0 CA E:ASP368 4.6 0.0 1.0 CB E:ASN312 4.7 0.1 1.0 CB E:VAL367 4.7 95.1 1.0 OD2 E:ASP368 4.8 0.6 1.0 OH E:TYR255 4.8 78.6 1.0 CA E:PHE314 4.8 0.2 1.0 CE2 E:TYR255 4.9 93.4 1.0 CB E:ALA313 5.0 0.4 1.0 C E:ASN312 5.0 0.2 1.0

Calcium binding site 2 out of 4 in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ F:Ca401 b:0.4 occ:1.00 OD2 F:ASP264 2.4 0.3 1.0 OD1 F:ASP264 2.4 0.9 1.0 O F:VAL367 2.4 0.4 1.0 OD1 F:ASN312 2.4 0.4 1.0 O F:ALA313 2.4 0.8 1.0 CG F:ASP264 2.6 0.2 1.0 C F:VAL367 3.4 0.9 1.0 CG F:ASN312 3.5 0.7 1.0 C F:ALA313 3.6 0.9 1.0 N F:VAL367 3.8 0.8 1.0 N F:ALA313 4.0 0.2 1.0 CB F:ASP264 4.0 0.7 1.0 CA F:VAL367 4.0 0.1 1.0 ND2 F:ASN312 4.1 0.6 1.0 CA F:ALA313 4.3 0.6 1.0 O F:LEU265 4.4 0.3 1.0 CB F:VAL367 4.4 0.4 1.0 N F:ASP368 4.5 0.3 1.0 OD1 F:ASP368 4.5 77.2 1.0 OH F:TYR255 4.6 87.3 1.0 N F:PHE314 4.6 0.1 1.0 CA F:ASP368 4.8 0.0 1.0 CB F:ASN312 4.8 0.9 1.0 CA F:PHE314 4.9 0.8 1.0 CG F:ASP368 4.9 84.2 1.0 C F:ALA366 4.9 0.8 1.0 CE2 F:TYR255 5.0 92.5 1.0

Calcium binding site 3 out of 4 in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ G:Ca401 b:98.8 occ:1.00 OD2 G:ASP264 2.4 0.9 1.0 OD1 G:ASP264 2.4 0.4 1.0 O G:VAL367 2.4 0.1 1.0 OD1 G:ASN312 2.4 98.0 1.0 O G:ALA313 2.4 98.5 1.0 CG G:ASP264 2.6 0.7 1.0 CG G:ASN312 3.5 0.5 1.0 C G:VAL367 3.5 0.8 1.0 C G:ALA313 3.6 99.1 1.0 ND2 G:ASN312 4.0 0.5 1.0 N G:ALA313 4.1 99.3 1.0 CB G:ASP264 4.1 0.6 1.0 OD1 G:ASP368 4.1 0.8 1.0 O G:LEU265 4.2 0.7 1.0 N G:VAL367 4.2 0.8 1.0 OH G:TYR255 4.3 66.6 1.0 CA G:VAL367 4.3 0.0 1.0 CA G:ALA313 4.4 98.3 1.0 N G:ASP368 4.5 0.2 1.0 N G:PHE314 4.5 81.8 1.0 CB G:VAL367 4.6 0.1 1.0 CA G:ASP368 4.7 0.4 1.0 CG G:ASP368 4.7 0.2 1.0 CA G:PHE314 4.7 0.6 1.0 CB G:ASN312 4.8 78.1 1.0 CE2 G:TYR255 4.9 78.7 1.0

Calcium binding site 4 out of 4 in the FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of FLRT3 Lrr Domain in Complex with LPHN3 Olfactomedin Domain within 5.0Å range: probe atom residue distance (Å) B Occ H:Ca401 b:0.3 occ:1.00 OD2 H:ASP264 2.4 82.6 1.0 OD1 H:ASP264 2.4 93.7 1.0 O H:VAL367 2.4 0.7 1.0 OD1 H:ASN312 2.4 0.7 1.0 O H:ALA313 2.4 72.3 1.0 CG H:ASP264 2.6 90.0 1.0 C H:VAL367 3.4 1.0 1.0 CG H:ASN312 3.4 0.4 1.0 C H:ALA313 3.6 72.2 1.0 N H:VAL367 3.8 0.9 1.0 ND2 H:ASN312 3.8 0.6 1.0 OD1 H:ASP368 3.9 0.0 1.0 CA H:VAL367 4.0 0.2 1.0 CB H:ASP264 4.0 92.4 1.0 N H:ALA313 4.0 0.0 1.0 CB H:VAL367 4.3 0.7 1.0 CG H:ASP368 4.4 0.5 1.0 N H:ASP368 4.4 0.3 1.0 O H:LEU265 4.4 92.3 1.0 CA H:ALA313 4.4 71.8 1.0 OH H:TYR255 4.5 60.1 1.0 N H:PHE314 4.6 90.9 1.0 CA H:ASP368 4.6 0.5 1.0 OD2 H:ASP368 4.7 0.0 1.0 CE2 H:TYR255 4.7 60.9 1.0 CB H:ASN312 4.7 0.3 1.0 CA H:PHE314 4.8 94.9 1.0 CB H:PHE314 4.9 87.4 1.0 CD1 H:ILE275 5.0 74.4 1.0

Y.C.Lu, O.V.Nazarko, R.Sando, G.S.Salzman, T.C.Sudhof, D.Arac. Structural Basis of Latrophilin-Flrt-UNC5 Interaction in Cell Adhesion. Structure V. 23 1678 2015.
ISSN: ISSN 0969-2126
PubMed: 26235030
DOI: 10.1016/J.STR.2015.06.024