Calcium in PDB 5oy9: Vsv G CR3

The structure of Vsv G CR3, PDB code: 5oy9 was solved by A.A.Albertini, L.Belot, P.Legrand, Y.Gaudin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.85 / 3.60
Space group	P 6 2 2
Cell size a, b, c (Å), α, β, γ (°)	122.350, 122.350, 197.810, 90.00, 90.00, 120.00
R / Rfree (%)	23.6 / 26.8

The binding sites of Calcium atom in the Vsv G CR3 (pdb code 5oy9). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Vsv G CR3, PDB code: 5oy9:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Vsv G CR3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vsv G CR3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:0.1 occ:0.57 OE1 A:GLU286 3.9 0.4 1.0 OE2 A:GLU286 4.2 0.3 1.0 OG A:SER282 4.4 0.9 1.0 CD A:GLU286 4.4 0.4 1.0 CD2 A:LEU283 4.7 0.1 1.0 CD1 A:LEU279 4.9 0.4 1.0 CB A:SER282 4.9 0.7 1.0

Calcium binding site 2 out of 4 in the Vsv G CR3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vsv G CR3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca505 b:0.8 occ:1.00 O A:TRP360 2.6 0.8 1.0 C A:TRP360 3.7 0.1 1.0 N A:TRP360 4.1 0.4 1.0 CA A:TRP360 4.5 0.7 1.0 N A:ALA361 4.7 0.2 1.0 CB A:TRP360 4.9 0.8 1.0 C A:ASP359 5.0 0.3 1.0 OD1 A:ASP359 5.0 0.8 1.0

Calcium binding site 3 out of 4 in the Vsv G CR3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Vsv G CR3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca506 b:0.8 occ:1.00 OD1 A:ASP274 3.2 0.2 1.0 OD2 A:ASP274 3.7 0.0 1.0 CG A:ASP274 3.9 0.2 1.0

Calcium binding site 4 out of 4 in the Vsv G CR3


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Vsv G CR3 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca1001 b:0.5 occ:1.00 O D:PHE105 2.3 0.9 1.0 OE2 D:GLU119 2.5 0.5 1.0 OD2 D:ASP112 2.5 0.2 1.0 O D:ASP110 2.7 0.5 1.0 OD2 D:ASP118 2.8 0.7 1.0 OD1 D:ASP108 2.9 0.8 1.0 CB D:ASP112 3.3 0.4 1.0 CG D:ASP112 3.3 0.0 1.0 CD D:GLU119 3.4 0.7 1.0 C D:PHE105 3.5 0.9 1.0 OE1 D:GLU119 3.7 0.8 1.0 N D:ASP112 3.8 0.4 1.0 C D:ASP110 3.9 0.3 1.0 CB D:PHE105 3.9 1.0 1.0 CG D:ASP118 3.9 0.7 1.0 CG D:ASP108 4.0 0.8 1.0 CA D:PHE105 4.1 0.3 1.0 CA D:ASP112 4.2 0.2 1.0 OD2 D:ASP108 4.4 0.8 1.0 CB D:ASP118 4.4 0.7 1.0 CB D:ASP110 4.4 0.6 1.0 OD1 D:ASP112 4.5 0.1 1.0 N D:VAL106 4.5 0.3 1.0 CA D:ASP110 4.5 0.9 1.0 N D:ASP110 4.5 0.2 1.0 CG D:GLU119 4.6 0.6 1.0 CD1 D:ILE101 4.6 0.9 1.0 CA D:VAL106 4.7 0.4 1.0 NZ A:LYS47 4.7 0.9 1.0 N D:ASP108 4.9 0.0 1.0 C D:ARG111 4.9 0.9 1.0 N D:ARG111 4.9 0.5 1.0 CG D:PHE105 4.9 0.1 1.0 N D:CYS107 4.9 0.8 1.0 OD1 D:ASP118 5.0 0.5 1.0

J.Nikolic, L.Belot, H.Raux, P.Legrand, Y.Gaudin, A.A Albertini. Structural Basis For the Recognition of Ldl-Receptor Family Members By Vsv Glycoprotein. Nat Commun V. 9 1029 2018.
ISSN: ESSN 2041-1723
PubMed: 29531262
DOI: 10.1038/S41467-018-03432-4