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Calcium in PDB 2w0c: X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2

Protein crystallography data

The structure of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2, PDB code: 2w0c was solved by N.G.A.Abrescia, J.M.Grimes, H.M.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) 96.00 / 7.00
Space group C 1 2 1 24
Cell size a, b, c (Å), α, β, γ (°) 946.900, 677.600, 1067.600, 90.00, 102.90, 90.00
R / Rfree (%) 41.9 / n/a

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Calcium atom in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 (pdb code 2w0c). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 11 binding sites of Calcium where determined in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2, PDB code: 2w0c:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 11 in 2w0c

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Calcium binding site 1 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1270

b:40.0
occ:1.00
O A:ALA105 2.5 40.0 1.0
O A:PRO141 2.6 40.0 1.0
O A:TRP143 2.8 40.0 1.0
O A:MET103 3.1 40.0 1.0
CD1 A:LEU144 3.3 40.0 1.0
N A:TRP143 3.6 40.0 1.0
C A:TRP143 3.7 40.0 1.0
C A:ALA105 3.7 40.0 1.0
C A:PRO141 3.7 40.0 1.0
CB A:SER142 3.8 40.0 1.0
C A:PHE104 3.9 40.0 1.0
N A:ALA105 3.9 40.0 1.0
C A:SER142 3.9 40.0 1.0
C A:MET103 3.9 40.0 1.0
CA A:TRP143 4.1 40.0 1.0
OG A:SER142 4.2 40.0 1.0
CA A:SER142 4.2 40.0 1.0
O A:PHE104 4.2 40.0 1.0
CA A:PHE104 4.2 40.0 1.0
O A:ALA140 4.3 40.0 1.0
CA A:ALA105 4.4 40.0 1.0
N A:SER142 4.4 40.0 1.0
N A:PHE104 4.4 40.0 1.0
N A:GLY107 4.5 40.0 1.0
O A:SER142 4.5 40.0 1.0
CB A:TRP143 4.6 40.0 1.0
N A:LEU144 4.7 40.0 1.0
N A:LEU106 4.8 40.0 1.0
CG A:LEU144 4.8 40.0 1.0
CA A:PRO141 4.8 40.0 1.0
CA A:MET103 5.0 40.0 1.0
O A:ARG102 5.0 40.0 1.0

Calcium binding site 2 out of 11 in 2w0c

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Calcium binding site 2 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1270

b:40.0
occ:1.00
O B:ALA105 2.6 40.0 1.0
O B:TRP143 2.6 40.0 1.0
O B:PRO141 2.7 40.0 1.0
O B:MET103 2.8 40.0 1.0
CD1 B:LEU144 3.1 40.0 1.0
C B:TRP143 3.5 40.0 1.0
N B:TRP143 3.6 40.0 1.0
C B:ALA105 3.7 40.0 1.0
C B:PRO141 3.8 40.0 1.0
C B:PHE104 3.8 40.0 1.0
CB B:SER142 3.8 40.0 1.0
C B:MET103 3.8 40.0 1.0
C B:SER142 3.9 40.0 1.0
N B:ALA105 3.9 40.0 1.0
CA B:TRP143 4.0 40.0 1.0
O B:PHE104 4.1 40.0 1.0
CA B:PHE104 4.1 40.0 1.0
OG B:SER142 4.2 40.0 1.0
CA B:SER142 4.2 40.0 1.0
N B:PHE104 4.4 40.0 1.0
O B:ALA140 4.4 40.0 1.0
CA B:ALA105 4.4 40.0 1.0
O B:SER142 4.4 40.0 1.0
N B:SER142 4.4 40.0 1.0
CB B:TRP143 4.5 40.0 1.0
N B:LEU144 4.6 40.0 1.0
CG B:LEU144 4.6 40.0 1.0
N B:GLY107 4.6 40.0 1.0
N B:LEU106 4.8 40.0 1.0
CA B:PRO141 4.9 40.0 1.0
CA B:LEU144 4.9 40.0 1.0
CA B:MET103 5.0 40.0 1.0

Calcium binding site 3 out of 11 in 2w0c

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Calcium binding site 3 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1270

b:40.0
occ:1.00
O C:TRP143 2.6 40.0 1.0
O C:MET103 2.7 40.0 1.0
O C:ALA105 2.7 40.0 1.0
O C:PRO141 2.7 40.0 1.0
CD1 C:LEU144 3.2 40.0 1.0
C C:TRP143 3.5 40.0 1.0
N C:TRP143 3.6 40.0 1.0
CZ3 Q:TRP30 3.6 40.0 1.0
C C:MET103 3.7 40.0 1.0
C C:PHE104 3.8 40.0 1.0
C C:ALA105 3.8 40.0 1.0
CB C:SER142 3.8 40.0 1.0
CH2 Q:TRP30 3.8 40.0 1.0
C C:PRO141 3.9 40.0 1.0
C C:SER142 3.9 40.0 1.0
N C:ALA105 3.9 40.0 1.0
CA C:TRP143 4.0 40.0 1.0
CA C:PHE104 4.0 40.0 1.0
O C:PHE104 4.1 40.0 1.0
OG C:SER142 4.2 40.0 1.0
CA C:SER142 4.2 40.0 1.0
N C:PHE104 4.3 40.0 1.0
O C:SER142 4.4 40.0 1.0
CA C:ALA105 4.4 40.0 1.0
CB C:TRP143 4.4 40.0 1.0
N C:SER142 4.5 40.0 1.0
O C:ALA140 4.5 40.0 1.0
N C:LEU144 4.6 40.0 1.0
CG C:LEU144 4.6 40.0 1.0
CE3 Q:TRP30 4.7 40.0 1.0
CA C:MET103 4.7 40.0 1.0
N C:GLY107 4.8 40.0 1.0
N C:LEU106 4.9 40.0 1.0
CA C:LEU144 4.9 40.0 1.0
O C:ARG102 5.0 40.0 1.0
CA C:PRO141 5.0 40.0 1.0
CZ2 Q:TRP30 5.0 40.0 1.0

Calcium binding site 4 out of 11 in 2w0c

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Calcium binding site 4 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1270

b:40.0
occ:1.00
O D:TRP143 2.6 40.0 1.0
O D:MET103 2.7 40.0 1.0
O D:ALA105 2.7 40.0 1.0
O D:PRO141 2.7 40.0 1.0
CD1 D:LEU144 3.2 40.0 1.0
C D:TRP143 3.5 40.0 1.0
N D:TRP143 3.6 40.0 1.0
C D:MET103 3.7 40.0 1.0
C D:PHE104 3.8 40.0 1.0
C D:ALA105 3.8 40.0 1.0
CB D:SER142 3.8 40.0 1.0
C D:PRO141 3.9 40.0 1.0
C D:SER142 3.9 40.0 1.0
N D:ALA105 3.9 40.0 1.0
CA D:TRP143 4.0 40.0 1.0
CA D:PHE104 4.0 40.0 1.0
O D:PHE104 4.1 40.0 1.0
OG D:SER142 4.2 40.0 1.0
CA D:SER142 4.2 40.0 1.0
N D:PHE104 4.3 40.0 1.0
O D:SER142 4.4 40.0 1.0
CA D:ALA105 4.4 40.0 1.0
CB D:TRP143 4.4 40.0 1.0
N D:SER142 4.5 40.0 1.0
O D:ALA140 4.5 40.0 1.0
N D:LEU144 4.6 40.0 1.0
CG D:LEU144 4.6 40.0 1.0
CA D:MET103 4.7 40.0 1.0
N D:GLY107 4.8 40.0 1.0
N D:LEU106 4.9 40.0 1.0
CA D:LEU144 4.9 40.0 1.0
O D:ARG102 5.0 40.0 1.0
CA D:PRO141 5.0 40.0 1.0

Calcium binding site 5 out of 11 in 2w0c

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Calcium binding site 5 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca1270

b:40.0
occ:1.00
O E:ALA105 2.5 40.0 1.0
O E:PRO141 2.6 40.0 1.0
O E:TRP143 2.8 40.0 1.0
CH2 R:TRP30 2.8 40.0 1.0
CZ3 R:TRP30 2.9 40.0 1.0
O E:MET103 3.1 40.0 1.0
CD1 E:LEU144 3.3 40.0 1.0
N E:TRP143 3.6 40.0 1.0
C E:TRP143 3.7 40.0 1.0
C E:ALA105 3.7 40.0 1.0
C E:PRO141 3.7 40.0 1.0
CB E:SER142 3.8 40.0 1.0
C E:PHE104 3.9 40.0 1.0
N E:ALA105 3.9 40.0 1.0
C E:SER142 3.9 40.0 1.0
C E:MET103 3.9 40.0 1.0
CZ2 R:TRP30 4.1 40.0 1.0
CA E:TRP143 4.1 40.0 1.0
OG E:SER142 4.2 40.0 1.0
CA E:SER142 4.2 40.0 1.0
O E:PHE104 4.2 40.0 1.0
CA E:PHE104 4.2 40.0 1.0
O E:ALA140 4.3 40.0 1.0
CE3 R:TRP30 4.3 40.0 1.0
CA E:ALA105 4.4 40.0 1.0
N E:SER142 4.4 40.0 1.0
N E:PHE104 4.4 40.0 1.0
N E:GLY107 4.5 40.0 1.0
O E:SER142 4.5 40.0 1.0
CB E:TRP143 4.6 40.0 1.0
N E:LEU144 4.7 40.0 1.0
N E:LEU106 4.8 40.0 1.0
CG E:LEU144 4.8 40.0 1.0
CA E:PRO141 4.8 40.0 1.0
CA E:MET103 5.0 40.0 1.0
O E:ARG102 5.0 40.0 1.0

Calcium binding site 6 out of 11 in 2w0c

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Calcium binding site 6 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca1270

b:40.0
occ:1.00
O F:ALA105 2.6 40.0 1.0
O F:TRP143 2.6 40.0 1.0
O F:PRO141 2.7 40.0 1.0
O F:MET103 2.8 40.0 1.0
CD1 F:LEU144 3.1 40.0 1.0
C F:TRP143 3.5 40.0 1.0
N F:TRP143 3.6 40.0 1.0
C F:ALA105 3.7 40.0 1.0
C F:PRO141 3.8 40.0 1.0
C F:PHE104 3.8 40.0 1.0
CB F:SER142 3.8 40.0 1.0
C F:MET103 3.8 40.0 1.0
C F:SER142 3.9 40.0 1.0
N F:ALA105 3.9 40.0 1.0
CA F:TRP143 4.0 40.0 1.0
O F:PHE104 4.1 40.0 1.0
CA F:PHE104 4.1 40.0 1.0
OG F:SER142 4.2 40.0 1.0
CA F:SER142 4.2 40.0 1.0
N F:PHE104 4.4 40.0 1.0
O F:ALA140 4.4 40.0 1.0
CA F:ALA105 4.4 40.0 1.0
O F:SER142 4.4 40.0 1.0
N F:SER142 4.4 40.0 1.0
CB F:TRP143 4.5 40.0 1.0
N F:LEU144 4.6 40.0 1.0
CG F:LEU144 4.6 40.0 1.0
N F:GLY107 4.6 40.0 1.0
N F:LEU106 4.8 40.0 1.0
CA F:PRO141 4.9 40.0 1.0
CA F:LEU144 4.9 40.0 1.0
CA F:MET103 5.0 40.0 1.0

Calcium binding site 7 out of 11 in 2w0c

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Calcium binding site 7 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca1270

b:40.0
occ:1.00
O G:ALA105 2.5 40.0 1.0
O G:PRO141 2.6 40.0 1.0
O G:TRP143 2.8 40.0 1.0
O G:MET103 3.1 40.0 1.0
CD1 G:LEU144 3.3 40.0 1.0
CZ3 P:TRP30 3.6 40.0 1.0
CH2 P:TRP30 3.6 40.0 1.0
N G:TRP143 3.6 40.0 1.0
C G:TRP143 3.7 40.0 1.0
C G:ALA105 3.7 40.0 1.0
C G:PRO141 3.7 40.0 1.0
CB G:SER142 3.8 40.0 1.0
C G:PHE104 3.9 40.0 1.0
C G:SER142 3.9 40.0 1.0
N G:ALA105 3.9 40.0 1.0
C G:MET103 3.9 40.0 1.0
CA G:TRP143 4.1 40.0 1.0
CA G:SER142 4.2 40.0 1.0
OG G:SER142 4.2 40.0 1.0
O G:PHE104 4.2 40.0 1.0
CA G:PHE104 4.2 40.0 1.0
O G:ALA140 4.3 40.0 1.0
CA G:ALA105 4.4 40.0 1.0
N G:SER142 4.4 40.0 1.0
N G:PHE104 4.4 40.0 1.0
N G:GLY107 4.5 40.0 1.0
O G:SER142 4.5 40.0 1.0
CB G:TRP143 4.6 40.0 1.0
N G:LEU144 4.7 40.0 1.0
N G:LEU106 4.8 40.0 1.0
CG G:LEU144 4.8 40.0 1.0
CA G:PRO141 4.8 40.0 1.0
CE3 P:TRP30 4.9 40.0 1.0
CZ2 P:TRP30 4.9 40.0 1.0
CA G:MET103 5.0 40.0 1.0
O G:ARG102 5.0 40.0 1.0

Calcium binding site 8 out of 11 in 2w0c

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Calcium binding site 8 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca1270

b:40.0
occ:1.00
O H:ALA105 2.6 40.0 1.0
O H:TRP143 2.6 40.0 1.0
O H:PRO141 2.7 40.0 1.0
O H:MET103 2.8 40.0 1.0
CD1 H:LEU144 3.1 40.0 1.0
C H:TRP143 3.5 40.0 1.0
N H:TRP143 3.6 40.0 1.0
C H:ALA105 3.7 40.0 1.0
C H:PRO141 3.8 40.0 1.0
C H:PHE104 3.8 40.0 1.0
CB H:SER142 3.8 40.0 1.0
C H:MET103 3.8 40.0 1.0
C H:SER142 3.9 40.0 1.0
N H:ALA105 3.9 40.0 1.0
CA H:TRP143 4.0 40.0 1.0
CA H:PHE104 4.1 40.0 1.0
O H:PHE104 4.1 40.0 1.0
OG H:SER142 4.2 40.0 1.0
CA H:SER142 4.2 40.0 1.0
N H:PHE104 4.4 40.0 1.0
O H:ALA140 4.4 40.0 1.0
CA H:ALA105 4.4 40.0 1.0
O H:SER142 4.4 40.0 1.0
N H:SER142 4.4 40.0 1.0
CB H:TRP143 4.5 40.0 1.0
N H:LEU144 4.6 40.0 1.0
CG H:LEU144 4.6 40.0 1.0
N H:GLY107 4.6 40.0 1.0
N H:LEU106 4.8 40.0 1.0
CA H:PRO141 4.9 40.0 1.0
CA H:LEU144 4.9 40.0 1.0
CA H:MET103 5.0 40.0 1.0

Calcium binding site 9 out of 11 in 2w0c

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Calcium binding site 9 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca1270

b:40.0
occ:1.00
O I:TRP143 2.6 40.0 1.0
O I:MET103 2.7 40.0 1.0
O I:ALA105 2.7 40.0 1.0
O I:PRO141 2.7 40.0 1.0
CD1 I:LEU144 3.2 40.0 1.0
C I:TRP143 3.5 40.0 1.0
CZ3 S:TRP30 3.5 40.0 1.0
N I:TRP143 3.6 40.0 1.0
C I:MET103 3.7 40.0 1.0
C I:PHE104 3.8 40.0 1.0
C I:ALA105 3.8 40.0 1.0
CB I:SER142 3.8 40.0 1.0
C I:SER142 3.9 40.0 1.0
C I:PRO141 3.9 40.0 1.0
N I:ALA105 3.9 40.0 1.0
CA I:TRP143 4.0 40.0 1.0
CA I:PHE104 4.0 40.0 1.0
CH2 S:TRP30 4.1 40.0 1.0
O I:PHE104 4.1 40.0 1.0
OG I:SER142 4.2 40.0 1.0
CA I:SER142 4.2 40.0 1.0
N I:PHE104 4.3 40.0 1.0
CE3 S:TRP30 4.3 40.0 1.0
O I:SER142 4.4 40.0 1.0
CA I:ALA105 4.4 40.0 1.0
CB I:TRP143 4.4 40.0 1.0
N I:SER142 4.5 40.0 1.0
O I:ALA140 4.5 40.0 1.0
N I:LEU144 4.6 40.0 1.0
CG I:LEU144 4.6 40.0 1.0
CA I:MET103 4.7 40.0 1.0
N I:GLY107 4.8 40.0 1.0
N I:LEU106 4.9 40.0 1.0
CA I:LEU144 4.9 40.0 1.0
O I:ARG102 5.0 40.0 1.0
CA I:PRO141 5.0 40.0 1.0

Calcium binding site 10 out of 11 in 2w0c

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Calcium binding site 10 out of 11 in the X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of X-Ray Structure of the Entire Lipid-Containing Bacteriophage PM2 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca1270

b:40.0
occ:1.00
O J:ALA105 2.5 40.0 1.0
O J:PRO141 2.6 40.0 1.0
O J:TRP143 2.8 40.0 1.0
O J:MET103 3.1 40.0 1.0
CD1 J:LEU144 3.3 40.0 1.0
N J:TRP143 3.6 40.0 1.0
C J:TRP143 3.7 40.0 1.0
C J:ALA105 3.7 40.0 1.0
C J:PRO141 3.7 40.0 1.0
CB J:SER142 3.8 40.0 1.0
C J:PHE104 3.9 40.0 1.0
N J:ALA105 3.9 40.0 1.0
C J:SER142 3.9 40.0 1.0
C J:MET103 3.9 40.0 1.0
CA J:TRP143 4.1 40.0 1.0
OG J:SER142 4.2 40.0 1.0
CA J:SER142 4.2 40.0 1.0
O J:PHE104 4.2 40.0 1.0
CA J:PHE104 4.2 40.0 1.0
O J:ALA140 4.3 40.0 1.0
CA J:ALA105 4.4 40.0 1.0
N J:SER142 4.4 40.0 1.0
N J:PHE104 4.4 40.0 1.0
N J:GLY107 4.5 40.0 1.0
O J:SER142 4.5 40.0 1.0
CB J:TRP143 4.6 40.0 1.0
N J:LEU144 4.7 40.0 1.0
N J:LEU106 4.8 40.0 1.0
CG J:LEU144 4.8 40.0 1.0
CA J:PRO141 4.8 40.0 1.0
CA J:MET103 5.0 40.0 1.0
O J:ARG102 5.0 40.0 1.0

Reference:

N.G.A.Abrescia, J.M.Grimes, H.M.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 03:54:49 2020

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