Calcium in PDB 2w4z: Caulobacter Bacteriophage 5

The structure of Caulobacter Bacteriophage 5, PDB code: 2w4z 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 / 3.60
Space group	H 3 16
Cell size a, b, c (Å), α, β, γ (°)	273.600, 273.600, 640.000, 90.00, 90.00, 120.00
R / Rfree (%)	29.6 / n/a

The binding sites of Calcium atom in the Caulobacter Bacteriophage 5 (pdb code 2w4z). 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, PDB code: 2w4z:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Caulobacter Bacteriophage 5


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1123 b:68.0 occ:1.00 OE1 A:GLU103 2.6 64.2 1.0 OD1 A:ASP100 2.7 63.1 1.0 OE2 A:GLU103 2.7 62.9 1.0 CD A:GLU103 3.0 62.5 1.0 CG A:ASP100 3.3 61.3 1.0 OD2 A:ASP100 3.5 62.3 1.0 CB A:ASP100 4.4 58.0 1.0 CG A:GLU103 4.5 60.7 1.0 CA A:ASP100 4.5 55.2 1.0 N A:ASP100 4.8 53.7 1.0

Calcium binding site 2 out of 4 in the Caulobacter Bacteriophage 5


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1123 b:79.1 occ:1.00 OD1 B:ASP100 2.2 68.5 1.0 OE2 B:GLU103 2.6 65.8 1.0 OE1 B:GLU103 2.9 64.2 1.0 CD B:GLU103 3.1 64.0 1.0 CG B:ASP100 3.4 66.6 1.0 OD2 B:ASP100 4.0 66.2 1.0 CB B:ASP100 4.6 64.4 1.0 CA B:ASP100 4.6 62.7 1.0 CG B:GLU103 4.6 62.6 1.0 O B:ALA96 4.8 66.0 1.0 N B:ASP100 4.9 62.1 1.0 OG B:SER99 5.0 64.0 1.0

Calcium binding site 3 out of 4 in the Caulobacter Bacteriophage 5


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1123 b:61.9 occ:1.00 O B:GLN25 2.2 59.7 1.0 OD2 A:ASP26 2.3 66.3 1.0 O A:GLN25 2.3 63.5 1.0 O C:GLN25 2.3 63.6 1.0 OD2 B:ASP26 2.3 61.9 1.0 OD1 C:ASP26 2.4 63.2 1.0 C B:GLN25 3.4 59.5 1.0 C A:GLN25 3.5 62.9 1.0 C C:GLN25 3.5 64.1 1.0 CG B:ASP26 3.5 61.5 1.0 CG A:ASP26 3.5 66.2 1.0 CG C:ASP26 3.6 64.2 1.0 NE2 C:GLN25 3.8 65.0 1.0 CA B:ASP26 3.8 58.8 1.0 CA A:ASP26 3.9 63.6 1.0 CA C:ASP26 3.9 63.8 1.0 N B:ASP26 4.0 59.0 1.0 N A:ASP26 4.1 63.0 1.0 N C:ASP26 4.2 63.5 1.0 CB B:ASP26 4.2 60.4 1.0 CG A:GLN25 4.2 63.2 1.0 NE2 B:GLN25 4.3 58.2 1.0 CB A:ASP26 4.3 64.7 1.0 CG C:GLN25 4.3 66.0 1.0 CB C:ASP26 4.3 63.6 1.0 CG B:GLN25 4.4 59.5 1.0 CD C:GLN25 4.4 65.8 1.0 OD1 A:ASP26 4.5 67.1 1.0 CD A:GLN25 4.5 62.6 1.0 OD2 C:ASP26 4.5 64.0 1.0 OD1 B:ASP26 4.5 62.7 1.0 CA B:GLN25 4.6 58.6 1.0 CD B:GLN25 4.6 59.4 1.0 NE2 A:GLN25 4.6 61.5 1.0 CA C:GLN25 4.6 64.1 1.0 CA A:GLN25 4.7 63.0 1.0 N C:GLN25 4.8 64.0 1.0 N B:GLN25 4.8 58.8 1.0 CB C:GLN25 4.9 65.2 1.0 O C:ASP26 4.9 65.3 1.0 N A:GLN25 4.9 62.4 1.0 CB B:GLN25 5.0 59.1 1.0 C C:ASP26 5.0 64.1 1.0

Calcium binding site 4 out of 4 in the Caulobacter Bacteriophage 5


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 within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca1124 b:78.8 occ:1.00 OD1 C:ASP100 2.5 67.7 1.0 OE1 C:GLU103 2.5 62.1 1.0 OE2 C:GLU103 2.9 60.4 1.0 CD C:GLU103 3.1 60.0 1.0 CG C:ASP100 3.3 65.4 1.0 OD2 C:ASP100 3.7 65.8 1.0 CA C:ASP100 4.3 60.5 1.0 CB C:ASP100 4.4 62.7 1.0 O C:ALA96 4.4 67.6 1.0 N C:ASP100 4.5 60.2 1.0 CG C:GLU103 4.5 58.2 1.0 OG C:SER99 4.8 61.9 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