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Calcium in PDB 2vvf: Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2

Protein crystallography data

The structure of Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2, PDB code: 2vvf 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) 41 / 2.5
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 163.990, 77.570, 127.850, 90.00, 90.00, 90.00
R / Rfree (%) 23.99 / 25.76

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2 (pdb code 2vvf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2, PDB code: 2vvf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 2vvf

Go back to Calcium Binding Sites List in 2vvf
Calcium binding site 1 out of 6 in the Crystal Structure of the Major Capsid Protein P2 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 Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1270

b:31.4
occ:1.00
 O A:ALA105 2.5 27.9 1.0
O A:PRO141 2.6 34.5 1.0
O A:TRP143 2.8 31.6 1.0
O A:MET103 3.1 28.4 1.0
CD1 A:LEU144 3.3 30.7 1.0
N A:TRP143 3.6 30.4 1.0
C A:TRP143 3.7 32.1 1.0
C A:ALA105 3.7 28.2 1.0
C A:PRO141 3.7 34.6 1.0
CB A:SER142 3.8 34.1 1.0
C A:PHE104 3.9 28.1 1.0
N A:ALA105 3.9 24.5 1.0
C A:SER142 3.9 33.5 1.0
C A:MET103 3.9 28.8 1.0
CA A:TRP143 4.1 30.3 1.0
OG A:SER142 4.2 44.9 1.0
CA A:SER142 4.2 30.4 1.0
O A:PHE104 4.2 27.6 1.0
CA A:PHE104 4.2 24.9 1.0
O A:ALA140 4.3 33.8 1.0
CA A:ALA105 4.4 24.2 1.0
N A:SER142 4.4 30.8 1.0
N A:PHE104 4.4 25.2 1.0
N A:GLY107 4.5 25.4 1.0
O A:SER142 4.5 32.5 1.0
CB A:TRP143 4.6 29.5 1.0
N A:LEU144 4.7 26.9 1.0
N A:LEU106 4.8 24.6 1.0
CG A:LEU144 4.8 30.6 1.0
CA A:PRO141 4.8 30.8 1.0
CA A:MET103 5.0 25.1 1.0
O A:ARG102 5.0 27.7 1.0

Calcium binding site 2 out of 6 in 2vvf

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Calcium binding site 2 out of 6 in the Crystal Structure of the Major Capsid Protein P2 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 Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1270

b:27.1
occ:1.00
 O B:ALA105 2.6 26.4 1.0
O B:TRP143 2.6 27.9 1.0
O B:PRO141 2.7 32.7 1.0
O B:MET103 2.8 28.0 1.0
CD1 B:LEU144 3.1 27.2 1.0
C B:TRP143 3.5 28.3 1.0
N B:TRP143 3.6 26.3 1.0
C B:ALA105 3.7 26.6 1.0
C B:PRO141 3.8 33.2 1.0
C B:PHE104 3.8 26.6 1.0
CB B:SER142 3.8 33.1 1.0
C B:MET103 3.8 28.2 1.0
C B:SER142 3.9 31.7 1.0
N B:ALA105 3.9 23.0 1.0
CA B:TRP143 4.0 25.6 1.0
CA B:PHE104 4.1 23.4 1.0
O B:PHE104 4.1 25.9 1.0
OG B:SER142 4.2 43.8 1.0
CA B:SER142 4.2 29.1 1.0
N B:PHE104 4.4 24.0 1.0
O B:ALA140 4.4 32.3 1.0
CA B:ALA105 4.4 22.8 1.0
O B:SER142 4.4 31.5 1.0
N B:SER142 4.4 29.6 1.0
CB B:TRP143 4.5 24.5 1.0
N B:LEU144 4.6 23.4 1.0
CG B:LEU144 4.6 27.1 1.0
N B:GLY107 4.6 23.8 1.0
N B:LEU106 4.8 22.9 1.0
CA B:PRO141 4.9 29.2 1.0
CA B:LEU144 4.9 22.6 1.0
CA B:MET103 5.0 25.1 1.0

Calcium binding site 3 out of 6 in 2vvf

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Calcium binding site 3 out of 6 in the Crystal Structure of the Major Capsid Protein P2 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 Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1270

b:23.8
occ:1.00
 O C:TRP143 2.6 32.8 1.0
O C:MET103 2.7 29.6 1.0
O C:ALA105 2.7 29.6 1.0
O C:PRO141 2.7 36.2 1.0
CD1 C:LEU144 3.2 33.2 1.0
C C:TRP143 3.5 33.3 1.0
N C:TRP143 3.6 30.7 1.0
C C:MET103 3.7 30.1 1.0
C C:PHE104 3.8 29.8 1.0
C C:ALA105 3.8 29.9 1.0
CB C:SER142 3.8 35.9 1.0
C C:PRO141 3.9 36.4 1.0
C C:SER142 3.9 34.9 1.0
N C:ALA105 3.9 26.2 1.0
CA C:TRP143 4.0 30.3 1.0
CA C:PHE104 4.0 26.6 1.0
O C:PHE104 4.1 29.3 1.0
OG C:SER142 4.2 46.8 1.0
CA C:SER142 4.2 32.1 1.0
N C:PHE104 4.3 26.9 1.0
O C:SER142 4.4 34.2 1.0
CA C:ALA105 4.4 25.9 1.0
CB C:TRP143 4.4 29.2 1.0
N C:SER142 4.5 32.6 1.0
O C:ALA140 4.5 35.5 1.0
N C:LEU144 4.6 29.1 1.0
CG C:LEU144 4.6 33.1 1.0
CA C:MET103 4.7 25.9 1.0
N C:GLY107 4.8 27.2 1.0
N C:LEU106 4.9 26.3 1.0
CA C:LEU144 4.9 28.5 1.0
O C:ARG102 5.0 29.1 1.0
CA C:PRO141 5.0 32.6 1.0

Calcium binding site 4 out of 6 in 2vvf

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Calcium binding site 4 out of 6 in the Crystal Structure of the Major Capsid Protein P2 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 Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1270

b:37.7
occ:1.00
 O D:TRP143 2.6 34.0 1.0
O D:PRO141 2.6 36.1 1.0
O D:ALA105 2.6 29.5 1.0
O D:MET103 3.0 30.5 1.0
CD1 D:LEU144 3.2 33.6 1.0
C D:TRP143 3.5 34.6 1.0
N D:TRP143 3.5 32.6 1.0
C D:PRO141 3.8 36.3 1.0
CB D:SER142 3.8 35.9 1.0
C D:ALA105 3.8 29.8 1.0
C D:SER142 3.8 35.3 1.0
C D:PHE104 3.8 29.8 1.0
C D:MET103 3.9 30.9 1.0
N D:ALA105 3.9 26.2 1.0
CA D:TRP143 4.0 32.6 1.0
CA D:PHE104 4.1 26.6 1.0
O D:PHE104 4.2 29.3 1.0
CA D:SER142 4.2 32.1 1.0
OG D:SER142 4.2 46.6 1.0
N D:PHE104 4.4 27.0 1.0
O D:ALA140 4.4 35.4 1.0
O D:SER142 4.4 34.3 1.0
N D:SER142 4.4 32.5 1.0
CA D:ALA105 4.4 25.9 1.0
CB D:TRP143 4.4 31.9 1.0
N D:LEU144 4.6 29.8 1.0
CG D:LEU144 4.7 33.5 1.0
N D:GLY107 4.7 27.1 1.0
N D:LEU106 4.9 26.3 1.0
CA D:PRO141 4.9 32.5 1.0
CA D:MET103 5.0 27.4 1.0
CA D:LEU144 5.0 29.0 1.0

Calcium binding site 5 out of 6 in 2vvf

Go back to Calcium Binding Sites List in 2vvf
Calcium binding site 5 out of 6 in the Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1270

b:32.7
occ:1.00
 O E:ALA105 2.6 25.2 1.0
O E:MET103 2.6 27.3 1.0
O E:TRP143 2.6 30.5 1.0
O E:PRO141 2.8 31.5 1.0
CD1 E:LEU144 3.2 31.6 1.0
C E:TRP143 3.6 31.1 1.0
C E:MET103 3.6 27.9 1.0
N E:TRP143 3.7 28.3 1.0
C E:ALA105 3.7 25.5 1.0
C E:PHE104 3.7 26.0 1.0
N E:ALA105 3.8 22.1 1.0
CB E:SER142 3.9 33.0 1.0
C E:PRO141 3.9 32.3 1.0
C E:SER142 4.0 32.0 1.0
CA E:PHE104 4.0 23.1 1.0
CA E:TRP143 4.1 28.0 1.0
O E:PHE104 4.1 25.5 1.0
N E:PHE104 4.2 23.9 1.0
CA E:ALA105 4.3 21.9 1.0
CA E:SER142 4.3 28.8 1.0
O E:ALA140 4.5 31.9 1.0
CB E:TRP143 4.5 27.0 1.0
O E:SER142 4.6 31.6 1.0
N E:SER142 4.6 29.0 1.0
N E:LEU144 4.6 27.6 1.0
N E:GLY107 4.7 23.2 1.0
CG E:LEU144 4.7 31.5 1.0
CA E:MET103 4.8 25.1 1.0
N E:LEU106 4.8 21.6 1.0
O E:ARG102 4.9 27.2 1.0
CB E:ALA105 5.0 22.6 1.0
CA E:LEU144 5.0 26.9 1.0
OG E:SER142 5.0 43.6 1.0

Calcium binding site 6 out of 6 in 2vvf

Go back to Calcium Binding Sites List in 2vvf
Calcium binding site 6 out of 6 in the Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of the Major Capsid Protein P2 From Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1270

b:34.4
occ:1.00
 OG F:SER142 2.5 49.3 1.0
O F:PRO141 2.6 37.7 1.0
O F:ALA105 2.6 31.5 1.0
O F:TRP143 2.7 36.8 1.0
O F:HOH2017 2.7 22.1 1.0
O F:MET103 3.0 33.3 1.0
CD1 F:LEU144 3.2 38.4 1.0
C F:TRP143 3.6 37.4 1.0
N F:TRP143 3.6 34.5 1.0
C F:PRO141 3.7 38.5 1.0
CB F:SER142 3.8 38.7 1.0
C F:ALA105 3.8 32.1 1.0
C F:SER142 3.8 38.3 1.0
C F:PHE104 3.9 32.4 1.0
C F:MET103 3.9 33.6 1.0
N F:ALA105 4.0 28.7 1.0
CA F:TRP143 4.1 34.1 1.0
CA F:SER142 4.2 34.9 1.0
O F:PHE104 4.2 31.7 1.0
CA F:PHE104 4.2 28.9 1.0
O F:ALA140 4.4 38.6 1.0
N F:SER142 4.4 35.1 1.0
O F:SER142 4.4 37.9 1.0
N F:PHE104 4.5 29.4 1.0
CA F:ALA105 4.5 28.5 1.0
CB F:TRP143 4.5 33.1 1.0
N F:LEU144 4.6 34.2 1.0
CG F:LEU144 4.6 38.3 1.0
N F:GLY107 4.6 29.4 1.0
CA F:PRO141 4.8 34.9 1.0
N F:LEU106 4.9 28.5 1.0
CA F:LEU144 5.0 33.7 1.0

Reference:

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
Page generated: Sat Dec 12 03:54:32 2020

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