Calcium in PDB 2vve: Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2

The structure of Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2, PDB code: 2vve was solved by N.G.A.Abrescia, J.M.Grimes, H.K.Kivela, R.Assenberg, G.C.Sutton, S.J.Butcher, J.K.H.Bamford, D.H.Bamford, D.I.Stuart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.00 / 1.77
Space group	P 4
Cell size a, b, c (Å), α, β, γ (°)	107.894, 107.894, 44.171, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 22.6

The structure of Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Calcium atom in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 (pdb code 2vve). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2, PDB code: 2vve:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2


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 the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1336 b:30.3 occ:1.00 O A:HOH2207 2.1 29.2 1.0 OD2 A:ASP295 2.3 33.5 1.0 O A:SER231 2.3 29.7 1.0 O A:HOH2256 2.4 24.3 1.0 O A:HOH2254 2.4 27.1 1.0 OD2 A:ASP293 2.5 19.3 1.0 OD1 A:ASP293 2.5 33.1 1.0 CG A:ASP293 2.9 28.7 1.0 CG A:ASP295 3.4 30.8 1.0 C A:SER231 3.5 27.7 1.0 CB A:ASP295 4.0 31.0 1.0 CB A:SER231 4.3 33.9 0.5 OD1 A:ASP295 4.3 34.9 1.0 N A:ILE232 4.4 27.1 1.0 CB A:SER231 4.4 32.6 0.5 O A:HOH2206 4.4 39.9 1.0 CA A:ILE232 4.4 22.8 1.0 CB A:ASP293 4.4 20.9 1.0 OG A:SER231 4.4 22.4 0.5 CA A:SER231 4.4 31.9 0.5 CA A:SER231 4.4 31.2 0.5 O A:HOH2255 4.5 27.7 1.0 N A:SER233 4.5 25.9 1.0 N A:ASP295 4.6 25.6 1.0 OG A:SER233 4.9 29.5 1.0 N A:SER231 4.9 31.7 1.0 C A:ILE232 4.9 23.3 1.0 CA A:ASP295 5.0 28.3 1.0

Calcium binding site 2 out of 4 in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2


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 the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1336 b:23.8 occ:1.00 O B:HOH2202 2.1 27.2 1.0 O B:HOH2153 2.3 22.5 1.0 O B:SER231 2.3 24.9 1.0 O B:HOH2205 2.4 25.5 1.0 OD2 B:ASP295 2.4 22.4 1.0 OD1 B:ASP293 2.5 21.8 1.0 OD2 B:ASP293 2.6 15.3 1.0 CG B:ASP293 2.9 13.9 1.0 C B:SER231 3.4 22.1 1.0 CG B:ASP295 3.5 32.4 1.0 CB B:ASP295 4.1 28.6 1.0 N B:ILE232 4.2 21.2 1.0 CA B:ILE232 4.2 19.5 1.0 O B:HOH2150 4.2 26.3 1.0 CB B:SER231 4.3 28.2 0.5 CB B:SER231 4.3 28.9 0.5 O B:HOH2108 4.3 45.4 1.0 CA B:SER231 4.4 28.5 0.5 CA B:SER231 4.4 28.1 0.5 CB B:ASP293 4.4 15.4 1.0 O B:HOH2149 4.4 31.5 1.0 N B:SER233 4.5 15.6 1.0 OD1 B:ASP295 4.5 28.2 1.0 OG B:SER231 4.6 34.1 0.5 N B:ASP295 4.6 22.8 1.0 OG B:SER233 4.7 20.4 1.0 O B:HOH2203 4.7 25.7 1.0 C B:ILE232 4.8 16.5 1.0 CG A:MET275 4.9 20.6 1.0 N B:SER231 4.9 26.6 1.0 CA B:ASP295 5.0 26.6 1.0

Calcium binding site 3 out of 4 in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2


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 the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1337 b:43.2 occ:1.00 OD2 B:ASP303 2.5 34.4 1.0 O B:HOH2212 2.6 39.0 1.0 OD1 B:ASP303 2.6 45.1 1.0 O B:HOH2210 2.8 30.6 1.0 CG B:ASP303 2.9 42.2 1.0 O B:GLN301 3.4 24.4 1.0 CA B:CA1338 3.9 28.7 1.0 CB B:GLN301 4.1 34.4 1.0 C B:GLN301 4.2 30.6 1.0 CB B:ASP303 4.4 32.6 1.0 CA B:GLN301 4.5 31.1 1.0 O B:HOH2211 4.7 33.6 1.0 O B:HIS302 4.8 27.9 1.0 CG B:GLN301 4.9 40.0 1.0 C B:HIS302 5.0 28.3 1.0

Calcium binding site 4 out of 4 in the Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Stem and Receptor Binding Domain of the Spike Protein P1 From Bacteriophage PM2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1338 b:28.7 occ:1.00 O B:GLN301 2.4 24.4 1.0 OD2 B:ASP306 2.4 24.4 1.0 OD2 B:ASP303 2.4 34.4 1.0 O B:HOH2210 2.5 30.6 1.0 O B:HOH2209 2.6 36.0 1.0 CG B:ASP306 3.4 29.9 1.0 C B:GLN301 3.6 30.6 1.0 CG B:ASP303 3.6 42.2 1.0 OD1 B:ASP306 3.6 34.5 1.0 CA B:CA1337 3.9 43.2 1.0 N B:ASP303 4.1 29.2 1.0 CB B:ASP303 4.2 32.6 1.0 CA B:HIS302 4.2 22.7 1.0 N B:HIS302 4.3 24.7 1.0 C B:HIS302 4.4 28.3 1.0 CB B:GLN301 4.4 34.4 1.0 O B:HOH2113 4.5 41.9 1.0 OD1 B:ASP303 4.6 45.1 1.0 CA B:GLN301 4.6 31.1 1.0 CB B:ASP306 4.7 22.7 1.0 CA B:ASP303 4.8 30.0 1.0 O B:VAL300 5.0 29.7 1.0 O B:HOH2115 5.0 26.9 1.0

N.G.A.Abrescia, J.M.Grimes, H.K.Kivela, R.Assenberg, G.C.Sutton, S.J.Butcher, J.K.H.Bamford, D.H.Bamford, D.I.Stuart. Insights Into Virus Evolution and Membrane Biogenesis From the Structure of the Marine Lipid- Containing Bacteriophage PM2. Mol.Cell V. 31 749 2008.
ISSN: ISSN 1097-2765
PubMed: 18775333
DOI: 10.1016/J.MOLCEL.2008.06.026