Calcium in PDB 4nwv: Crystal Structure of Orsay Virus-Like Particle

The structure of Crystal Structure of Orsay Virus-Like Particle, PDB code: 4nwv was solved by Y.J.Tao, Y.R.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 3.25
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	402.197, 369.862, 410.511, 90.00, 90.00, 90.00
R / Rfree (%)	27.8 / 27.9

The binding sites of Calcium atom in the Crystal Structure of Orsay Virus-Like Particle (pdb code 4nwv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Orsay Virus-Like Particle, PDB code: 4nwv:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Orsay Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Orsay Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:94.2 occ:1.00 OE1 A:GLN92 2.2 38.4 1.0 OD1 C:ASP122 2.5 53.4 1.0 OD1 C:ASP125 2.8 0.1 1.0 OE1 A:GLU166 3.3 0.5 1.0 CD A:GLN92 3.4 41.6 1.0 CG C:ASP125 3.6 0.3 1.0 CB A:GLU166 3.6 70.0 1.0 OD2 C:ASP125 3.7 93.9 1.0 CG C:ASP122 3.7 52.9 1.0 NH1 C:ARG176 4.1 32.0 1.0 CD A:GLU166 4.1 0.3 1.0 O A:GLN92 4.2 25.0 1.0 N A:GLU166 4.3 24.6 1.0 CG A:GLN92 4.3 37.5 1.0 OG1 A:THR165 4.3 30.6 1.0 NE2 A:GLN92 4.3 40.2 1.0 CB C:ASP122 4.4 47.9 1.0 O A:GLU166 4.4 21.0 1.0 CA A:GLU166 4.5 31.1 1.0 CG A:GLU166 4.5 90.3 1.0 NE A:ARG213 4.5 81.1 1.0 CD1 A:TYR164 4.5 38.0 1.0 N A:THR165 4.6 31.8 1.0 CB A:TYR164 4.7 37.0 1.0 OD2 C:ASP122 4.7 51.4 1.0 CA A:GLN92 4.8 32.5 1.0 C A:GLU166 4.8 23.1 1.0 C A:THR165 4.8 29.9 1.0 CB C:ASP125 4.9 0.6 1.0 CZ C:ARG176 5.0 31.7 1.0 C A:GLN92 5.0 27.4 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Orsay Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Orsay Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:80.2 occ:1.00 OE1 B:GLN92 2.6 39.2 1.0 OD2 A:ASP122 2.7 43.2 1.0 OD1 A:ASP125 2.9 0.9 1.0 OE1 B:GLU166 3.3 0.6 1.0 CG A:ASP125 3.7 0.8 1.0 CD B:GLN92 3.7 34.6 1.0 CG A:ASP122 3.7 41.5 1.0 OD2 A:ASP125 3.7 0.3 1.0 CD B:GLU166 3.8 0.1 1.0 CB B:GLU166 3.9 72.8 1.0 CB A:ASP122 4.2 39.3 1.0 CG B:GLU166 4.3 96.4 1.0 NH2 A:ARG176 4.3 30.3 1.0 OG1 B:THR165 4.5 18.2 1.0 CG B:GLN92 4.5 32.7 1.0 OE2 B:GLU166 4.5 0.5 1.0 O B:GLN92 4.6 24.3 1.0 N B:GLU166 4.6 24.1 1.0 NE2 B:GLN92 4.7 33.5 1.0 OD1 A:ASP122 4.7 34.6 1.0 CA B:GLU166 4.8 34.1 1.0 CA B:GLN92 4.9 27.0 1.0 O B:GLU166 4.9 29.1 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Orsay Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Orsay Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca901 b:73.0 occ:1.00 OE2 C:GLU166 2.7 0.2 1.0 OE1 C:GLN92 3.0 30.2 1.0 OD2 B:ASP122 3.2 55.5 1.0 OD2 B:ASP125 3.3 0.8 1.0 CG B:ASP122 3.3 48.8 1.0 OD1 B:ASP125 3.4 0.0 1.0 CD C:GLN92 3.5 35.9 1.0 CG C:GLU166 3.5 0.8 1.0 CD C:GLU166 3.5 0.0 1.0 NE2 C:GLN92 3.5 41.5 1.0 CG B:ASP125 3.6 0.8 1.0 CB B:ASP122 3.6 44.6 1.0 OD1 B:ASP122 3.9 43.6 1.0 NH2 B:ARG176 3.9 28.1 1.0 O C:GLN92 4.1 28.5 1.0 CA C:GLN92 4.3 32.5 1.0 CD1 C:TYR164 4.4 31.5 1.0 CB C:GLN92 4.5 32.4 1.0 OG1 C:THR165 4.5 23.7 1.0 CG C:GLN92 4.6 36.2 1.0 C C:GLN92 4.6 32.2 1.0 OE1 C:GLU166 4.7 0.2 1.0 CB C:GLU166 4.9 83.6 1.0 CB B:ASP125 4.9 98.2 1.0 CZ B:ARG176 5.0 25.2 1.0 N C:GLU166 5.0 16.8 1.0

Y.R.Guo, C.F.Hryc, J.Jakana, H.Jiang, D.Wang, W.Chiu, W.Zhong, Y.J.Tao. Crystal Structure of A Nematode-Infecting Virus. Proc.Natl.Acad.Sci.Usa V. 111 12781 2014.
ISSN: ISSN 0027-8424
PubMed: 25136116
DOI: 10.1073/PNAS.1407122111