Calcium in PDB 2w4y: Caulobacter Bacteriophage 5 - Virus-Like Particle

The structure of Caulobacter Bacteriophage 5 - Virus-Like Particle, PDB code: 2w4y was solved by P.Plevka, A.Kazaks, A.Dishlers, L.Liljas, K.Tars, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.90
Space group	C 1 2 1 7
Cell size a, b, c (Å), α, β, γ (°)	406.400, 342.600, 409.700, 90.00, 93.19, 90.00
R / Rfree (%)	27.8 / n/a

The binding sites of Calcium atom in the Caulobacter Bacteriophage 5 - Virus-Like Particle (pdb code 2w4y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Caulobacter Bacteriophage 5 - Virus-Like Particle, PDB code: 2w4y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Caulobacter Bacteriophage 5 - 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 Caulobacter Bacteriophage 5 - Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1123 b:38.4 occ:1.00 O B:GLN25 2.2 30.9 1.0 OD1 C:ASP26 2.2 40.8 1.0 O C:GLN25 2.2 35.1 1.0 OD2 A:ASP26 2.3 41.2 1.0 O A:GLN25 2.3 33.6 1.0 OD2 B:ASP26 2.4 38.3 1.0 C B:GLN25 3.4 30.7 1.0 CG C:ASP26 3.4 39.8 1.0 C C:GLN25 3.4 34.4 1.0 C A:GLN25 3.4 34.0 1.0 CG A:ASP26 3.5 39.8 1.0 CG B:ASP26 3.6 37.5 1.0 CA A:ASP26 3.9 35.2 1.0 CA B:ASP26 3.9 32.4 1.0 CA C:ASP26 3.9 35.8 1.0 N B:ASP26 4.1 31.0 1.0 N C:ASP26 4.1 34.5 1.0 N A:ASP26 4.1 34.5 1.0 CB C:ASP26 4.2 37.2 1.0 OE1 C:GLN25 4.2 38.3 1.0 CB A:ASP26 4.2 37.2 1.0 CB B:ASP26 4.3 34.2 1.0 CG B:GLN25 4.3 34.1 1.0 CG A:GLN25 4.3 35.8 1.0 CG C:GLN25 4.3 37.0 1.0 OD2 C:ASP26 4.3 38.5 1.0 OE1 A:GLN25 4.4 38.3 1.0 OD1 A:ASP26 4.4 37.6 1.0 CD A:GLN25 4.5 35.3 1.0 OE1 B:GLN25 4.5 36.3 1.0 CD C:GLN25 4.5 37.2 1.0 CA B:GLN25 4.5 30.6 1.0 OD1 B:ASP26 4.5 37.6 1.0 CA C:GLN25 4.6 34.4 1.0 CD B:GLN25 4.6 34.2 1.0 CA A:GLN25 4.7 33.8 1.0 N B:GLN25 4.8 29.8 1.0 N C:GLN25 4.8 33.6 1.0 CB B:GLN25 4.9 31.5 1.0 N A:GLN25 4.9 33.2 1.0 CB C:GLN25 4.9 35.1 1.0

Calcium binding site 2 out of 4 in the Caulobacter Bacteriophage 5 - 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 Caulobacter Bacteriophage 5 - Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1124 b:42.5 occ:1.00 OD1 A:ASP100 2.5 45.2 1.0 OE1 A:GLU103 2.6 37.6 1.0 OE2 A:GLU103 2.7 37.7 1.0 CD A:GLU103 3.0 36.1 1.0 CG A:ASP100 3.3 40.7 1.0 OD2 A:ASP100 3.6 43.3 1.0 CG A:GLU103 4.5 32.5 1.0 CB A:ASP100 4.5 36.0 1.0 CA A:ASP100 4.5 32.2 1.0 N A:ASP100 4.8 31.8 1.0 O A:ALA96 4.9 32.9 1.0

Calcium binding site 3 out of 4 in the Caulobacter Bacteriophage 5 - 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 Caulobacter Bacteriophage 5 - Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1123 b:49.5 occ:1.00 OD1 B:ASP100 2.3 46.6 1.0 OE2 B:GLU103 2.6 39.0 1.0 OE1 B:GLU103 2.9 39.2 1.0 CD B:GLU103 3.1 37.5 1.0 CG B:ASP100 3.4 44.1 1.0 OD2 B:ASP100 4.0 46.8 1.0 CB B:ASP100 4.6 40.2 1.0 CG B:GLU103 4.6 34.4 1.0 CA B:ASP100 4.6 36.9 1.0 O B:ALA96 4.8 40.1 1.0 N B:ASP100 4.9 37.0 1.0

Calcium binding site 4 out of 4 in the Caulobacter Bacteriophage 5 - Virus-Like Particle


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Caulobacter Bacteriophage 5 - Virus-Like Particle within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1123 b:49.4 occ:1.00 OD1 C:ASP100 2.4 50.5 1.0 OE1 C:GLU103 2.6 40.5 1.0 OE2 C:GLU103 2.9 39.9 1.0 CD C:GLU103 3.1 39.5 1.0 CG C:ASP100 3.4 47.3 1.0 OD2 C:ASP100 3.9 51.5 1.0 CA C:ASP100 4.5 39.5 1.0 O C:ALA96 4.5 41.6 1.0 CB C:ASP100 4.5 43.1 1.0 CG C:GLU103 4.6 36.5 1.0 N C:ASP100 4.7 39.0 1.0 OG C:SER99 4.8 41.1 1.0

P.Plevka, A.Kazaks, T.Voronkova, S.Kotelovica, A.Dishlers, L.Liljas, K.Tars. The Structure of Bacteriophage PHICB5 Reveals A Role of the Rna Genome and Metal Ions in Particle Stability and Assembly. J.Mol.Biol. V. 391 635 2009.
ISSN: ISSN 0022-2836
PubMed: 19559027
DOI: 10.1016/J.JMB.2009.06.047