Calcium in PDB 5oyl: Vsv G CR2

The structure of Vsv G CR2, PDB code: 5oyl 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)	29.98 / 2.25
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	90.040, 90.040, 515.780, 90.00, 90.00, 120.00
R / Rfree (%)	18.8 / 22.4

The binding sites of Calcium atom in the Vsv G CR2 (pdb code 5oyl). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Vsv G CR2, PDB code: 5oyl:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Vsv G CR2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Vsv G CR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca504 b:61.0 occ:1.00 OE2 A:GLU201 3.0 0.2 1.0 CG A:GLU201 3.2 0.8 1.0 CD A:GLU201 3.5 0.4 1.0 N A:GLY216 3.5 57.2 1.0 CA A:GLY216 3.6 60.4 1.0 N A:GLY202 3.7 70.4 1.0 CB A:THR214 3.9 46.6 1.0 CA A:GLY202 4.3 65.5 1.0 OG1 A:THR214 4.3 48.7 1.0 CB A:GLU201 4.4 96.2 1.0 O A:THR203 4.5 53.2 1.0 N A:GLY215 4.5 48.9 1.0 N A:THR203 4.5 62.1 1.0 CA A:GLU201 4.5 88.0 1.0 OE1 A:GLU201 4.6 0.3 1.0 C A:GLU201 4.6 78.5 1.0 CG2 A:THR214 4.7 37.5 1.0 C A:GLY215 4.7 53.7 1.0 C A:GLY216 4.9 57.5 1.0 CA A:THR214 4.9 45.0 1.0 C A:THR214 4.9 45.4 1.0

Calcium binding site 2 out of 2 in the Vsv G CR2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Vsv G CR2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Ca102 b:32.0 occ:1.00 OD2 D:ASP73 2.3 38.9 1.0 O D:GLN71 2.3 35.5 1.0 O D:TRP66 2.3 28.5 1.0 OE2 D:GLU80 2.4 41.4 1.0 OD2 D:ASP79 2.4 37.5 1.0 OD1 D:ASP69 2.5 35.8 1.0 CG D:ASP69 3.2 31.2 1.0 CG D:ASP73 3.3 38.8 1.0 CD D:GLU80 3.4 40.5 1.0 C D:GLN71 3.5 38.7 1.0 C D:TRP66 3.5 35.6 1.0 CG D:ASP79 3.5 34.4 1.0 OD2 D:ASP69 3.6 32.4 1.0 CG D:GLU80 3.9 35.4 1.0 CB D:ASP73 4.1 36.5 1.0 OD1 D:ASP73 4.1 41.6 1.0 N D:ASP73 4.1 40.4 1.0 N D:GLN71 4.1 36.6 1.0 CB D:ASP79 4.1 36.5 1.0 N D:ASP69 4.1 34.9 1.0 CA D:GLN71 4.2 31.6 1.0 CA D:TRP66 4.3 27.9 1.0 NZ A:LYS47 4.3 31.7 1.0 CB D:TRP66 4.4 27.1 1.0 CB D:ASP69 4.4 29.1 1.0 OE1 D:GLU80 4.5 42.9 1.0 N D:CYS68 4.5 40.8 1.0 N D:VAL72 4.5 40.5 1.0 CB D:GLN71 4.5 33.7 1.0 N D:ARG67 4.5 33.6 1.0 OD1 D:ASP79 4.6 35.2 1.0 CA D:ARG67 4.7 36.1 1.0 CA D:ASP69 4.7 36.5 1.0 CA D:VAL72 4.7 39.8 1.0 CA D:ASP73 4.8 37.2 1.0 N D:GLY70 4.8 35.5 1.0 O D:ASP79 4.8 34.9 1.0 C D:ARG67 4.8 40.4 1.0 C D:ASP79 4.8 41.1 1.0 C D:VAL72 4.9 40.9 1.0 C D:ASP69 4.9 38.0 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