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Calcium in PDB 8qkm: Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 60; Page 7, Binding sites: 61 - 70; Page 8, Binding sites: 71 - 80; Page 9, Binding sites: 81 - 90; Page 10, Binding sites: 91 - 92;

Binding sites:

The binding sites of Calcium atom in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna (pdb code 8qkm). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 92 binding sites of Calcium where determined in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna, PDB code: 8qkm:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 92 in 8qkm

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Calcium binding site 1 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:22.5
occ:1.00
 OD1 A:ASP55 2.4 13.6 1.0
OD1 m:ASP55 2.4 14.0 1.0
OD1 X:ASP55 2.4 13.9 1.0
CG A:ASP55 3.6 13.6 1.0
CG m:ASP55 3.6 14.0 1.0
CG X:ASP55 3.6 13.9 1.0
OG X:SER61 3.9 11.9 1.0
OG A:SER61 4.2 12.2 1.0
O A:GLY54 4.2 12.6 1.0
OD2 m:ASP55 4.2 14.0 1.0
OD2 A:ASP55 4.2 13.6 1.0
OG m:SER61 4.2 12.0 1.0
OD2 X:ASP55 4.3 13.9 1.0
O X:GLY54 4.4 12.6 1.0
CB X:SER61 4.4 11.9 1.0
O m:GLY54 4.5 12.5 1.0
CB m:SER61 4.5 12.0 1.0
CB A:SER61 4.5 12.2 1.0
CB A:ASP55 4.7 13.6 1.0
CB m:ASP55 4.7 14.0 1.0
CB X:ASP55 4.7 13.9 1.0
CA A:ASP55 4.8 13.6 1.0
CA m:ASP55 4.8 14.0 1.0
CA X:ASP55 4.8 13.9 1.0
C A:GLY54 4.9 12.6 1.0
C m:GLY54 5.0 12.5 1.0
C X:GLY54 5.0 12.6 1.0

Calcium binding site 2 out of 92 in 8qkm

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Calcium binding site 2 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca202

b:10.9
occ:1.00
 OD1 A:ASP194 2.3 12.2 1.0
OE1 m:GLU25 2.4 13.0 1.0
O A:SER61 2.4 12.2 1.0
O A:GLN64 2.4 11.0 1.0
CG A:ASP194 3.2 12.2 1.0
C A:GLN64 3.5 11.0 1.0
C A:SER61 3.5 12.2 1.0
CD m:GLU25 3.6 13.0 1.0
OD2 A:ASP194 3.8 12.2 1.0
CB m:GLU25 4.0 13.0 1.0
O A:ASP194 4.0 12.2 1.0
C A:ASP194 4.0 12.2 1.0
CA A:ASP194 4.0 12.2 1.0
CB A:ASP194 4.2 12.2 1.0
N A:GLN64 4.2 11.0 1.0
N A:SER61 4.3 12.2 1.0
CA A:SER61 4.3 12.2 1.0
CA A:GLN64 4.3 11.0 1.0
CG m:GLU25 4.4 13.0 1.0
CB A:SER61 4.4 12.2 1.0
O A:ALA195 4.4 14.8 1.0
OE2 m:GLU25 4.5 13.0 1.0
CB A:GLN64 4.5 11.0 1.0
N A:VAL65 4.5 9.0 1.0
N A:GLY62 4.6 12.3 1.0
N A:ALA195 4.7 14.8 1.0
CA A:GLY62 4.7 12.3 1.0
CA A:VAL65 4.7 9.0 1.0
C A:ALA195 4.8 14.8 1.0
CG1 A:VAL65 4.9 9.0 1.0
C A:GLY62 4.9 12.3 1.0

Calcium binding site 3 out of 92 in 8qkm

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Calcium binding site 3 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:9.9
occ:1.00
 OE1 2:GLU25 2.3 13.0 1.0
O B:SER61 2.3 11.9 1.0
OD1 B:ASP194 2.4 12.6 1.0
O B:GLN64 2.4 10.6 1.0
CG B:ASP194 3.3 12.6 1.0
C B:SER61 3.4 11.9 1.0
CD 2:GLU25 3.5 13.0 1.0
C B:GLN64 3.6 10.6 1.0
OD2 B:ASP194 3.8 12.6 1.0
O B:ASP194 4.0 12.6 1.0
C B:ASP194 4.0 12.6 1.0
CB 2:GLU25 4.1 13.0 1.0
N B:GLN64 4.1 10.6 1.0
CA B:ASP194 4.1 12.6 1.0
N B:SER61 4.2 11.9 1.0
CA B:SER61 4.3 11.9 1.0
CA B:GLN64 4.3 10.6 1.0
CB B:ASP194 4.3 12.6 1.0
OE2 2:GLU25 4.3 13.0 1.0
CG 2:GLU25 4.4 13.0 1.0
N B:GLY62 4.4 11.6 1.0
CB B:SER61 4.4 11.9 1.0
O B:ALA195 4.5 14.8 1.0
CB B:GLN64 4.5 10.6 1.0
CA B:GLY62 4.5 11.6 1.0
N B:VAL65 4.6 9.3 1.0
N B:ALA195 4.7 14.8 1.0
C B:GLY62 4.7 11.6 1.0
C B:ALA195 4.8 14.8 1.0
N B:ASP63 4.8 10.8 1.0
CA B:VAL65 4.9 9.3 1.0
CG1 B:VAL65 4.9 9.3 1.0

Calcium binding site 4 out of 92 in 8qkm

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Calcium binding site 4 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca202

b:13.1
occ:0.20
 O 7:THR138 2.3 16.1 1.0
O j:THR138 2.3 16.3 1.0
O J:THR138 2.3 16.0 1.0
O B:THR138 2.3 16.2 1.0
O T:THR138 2.3 16.0 1.0
C j:THR138 3.5 16.3 1.0
C B:THR138 3.5 16.2 1.0
C J:THR138 3.5 16.0 1.0
C 7:THR138 3.5 16.1 1.0
C T:THR138 3.5 16.0 1.0
CA J:GLY139 4.0 16.7 1.0
CA B:GLY139 4.1 16.6 1.0
CA T:GLY139 4.1 16.4 1.0
CA j:GLY139 4.1 16.5 1.0
CA 7:GLY139 4.2 16.3 1.0
N J:GLY139 4.2 16.7 1.0
N B:GLY139 4.2 16.6 1.0
N j:GLY139 4.2 16.5 1.0
N T:GLY139 4.3 16.4 1.0
N 7:GLY139 4.3 16.3 1.0
CA j:THR138 4.5 16.3 1.0
CA 7:THR138 4.6 16.1 1.0
CA B:THR138 4.6 16.2 1.0
CA T:THR138 4.6 16.0 1.0
CA J:THR138 4.6 16.0 1.0
CB 7:THR138 4.8 16.1 1.0
CB j:THR138 4.8 16.3 1.0
CB B:THR138 4.9 16.2 1.0
CB T:THR138 4.9 16.0 1.0
CB J:THR138 4.9 16.0 1.0

Calcium binding site 5 out of 92 in 8qkm

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Calcium binding site 5 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:11.2
occ:1.00
 OD1 C:ASP194 2.3 13.0 1.0
O C:SER61 2.3 12.2 1.0
O C:GLN64 2.4 11.2 1.0
OE1 4:GLU25 2.4 13.1 1.0
CG C:ASP194 3.3 13.0 1.0
C C:SER61 3.5 12.2 1.0
C C:GLN64 3.5 11.2 1.0
CD 4:GLU25 3.6 13.1 1.0
OD2 C:ASP194 3.9 13.0 1.0
O C:ASP194 4.0 13.0 1.0
CB 4:GLU25 4.1 13.1 1.0
C C:ASP194 4.1 13.0 1.0
N C:GLN64 4.1 11.2 1.0
CA C:ASP194 4.1 13.0 1.0
N C:SER61 4.2 12.2 1.0
CA C:SER61 4.3 12.2 1.0
CA C:GLN64 4.3 11.2 1.0
CB C:ASP194 4.3 13.0 1.0
CB C:SER61 4.3 12.2 1.0
CG 4:GLU25 4.5 13.1 1.0
OE2 4:GLU25 4.5 13.1 1.0
CB C:GLN64 4.5 11.2 1.0
N C:GLY62 4.5 11.9 1.0
N C:VAL65 4.6 9.6 1.0
CA C:GLY62 4.7 11.9 1.0
CG1 C:VAL65 4.7 9.6 1.0
N C:ALA195 4.8 16.0 1.0
CA C:VAL65 4.8 9.6 1.0
C C:GLY62 4.9 11.9 1.0
N C:ASP63 4.9 11.0 1.0
C C:ALA195 4.9 16.0 1.0

Calcium binding site 6 out of 92 in 8qkm

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Calcium binding site 6 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:13.0
occ:0.20
 O A:THR138 2.3 16.2 1.0
O D:THR138 2.3 16.4 1.0
O x:THR138 2.3 16.3 1.0
O k:THR138 2.3 16.2 1.0
O e:THR138 2.3 16.2 1.0
C D:THR138 3.5 16.4 1.0
C k:THR138 3.5 16.2 1.0
C x:THR138 3.5 16.3 1.0
C A:THR138 3.5 16.2 1.0
C e:THR138 3.5 16.2 1.0
CA x:GLY139 4.0 16.9 1.0
CA k:GLY139 4.1 16.6 1.0
CA e:GLY139 4.1 16.6 1.0
CA D:GLY139 4.1 16.6 1.0
CA A:GLY139 4.2 16.4 1.0
N x:GLY139 4.2 16.9 1.0
N k:GLY139 4.2 16.6 1.0
N D:GLY139 4.2 16.6 1.0
N e:GLY139 4.3 16.6 1.0
N A:GLY139 4.3 16.4 1.0
CA D:THR138 4.5 16.4 1.0
CA A:THR138 4.5 16.2 1.0
CA k:THR138 4.6 16.2 1.0
CA e:THR138 4.6 16.2 1.0
CA x:THR138 4.6 16.3 1.0
CB A:THR138 4.8 16.2 1.0
CB D:THR138 4.8 16.4 1.0
CB k:THR138 4.9 16.2 1.0
CB e:THR138 4.9 16.2 1.0
CB x:THR138 4.9 16.3 1.0

Calcium binding site 7 out of 92 in 8qkm

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Calcium binding site 7 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca202

b:10.3
occ:1.00
 O D:GLN64 2.3 10.6 1.0
OE1 h:GLU25 2.3 12.4 1.0
OD1 D:ASP194 2.3 12.3 1.0
O D:SER61 2.4 11.9 1.0
CG D:ASP194 3.4 12.3 1.0
C D:GLN64 3.4 10.6 1.0
CD h:GLU25 3.5 12.4 1.0
C D:SER61 3.6 11.9 1.0
CB h:GLU25 4.0 12.4 1.0
N D:GLN64 4.0 10.6 1.0
OD2 D:ASP194 4.1 12.3 1.0
O D:ASP194 4.1 12.3 1.0
C D:ASP194 4.1 12.3 1.0
CA D:ASP194 4.1 12.3 1.0
CA D:GLN64 4.2 10.6 1.0
O D:ALA195 4.2 14.6 1.0
CG h:GLU25 4.3 12.4 1.0
CB D:ASP194 4.4 12.3 1.0
CB D:GLN64 4.4 10.6 1.0
OE2 h:GLU25 4.4 12.4 1.0
CA D:SER61 4.4 11.9 1.0
N D:SER61 4.4 11.9 1.0
N D:VAL65 4.5 9.2 1.0
CB D:SER61 4.5 11.9 1.0
N D:GLY62 4.6 11.7 1.0
CA D:GLY62 4.7 11.7 1.0
CA D:VAL65 4.7 9.2 1.0
CG1 D:VAL65 4.8 9.2 1.0
N D:ALA195 4.8 14.6 1.0
C D:GLY62 4.8 11.7 1.0
N D:ASP63 4.9 11.2 1.0
C D:ALA195 5.0 14.6 1.0

Calcium binding site 8 out of 92 in 8qkm

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Calcium binding site 8 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:10.4
occ:1.00
 O E:SER61 2.3 11.9 1.0
OE1 f:GLU25 2.3 12.4 1.0
O E:GLN64 2.4 10.4 1.0
OD1 E:ASP194 2.4 12.1 1.0
CG E:ASP194 3.4 12.1 1.0
C E:SER61 3.5 11.9 1.0
CD f:GLU25 3.5 12.4 1.0
C E:GLN64 3.5 10.4 1.0
CB f:GLU25 3.9 12.4 1.0
OD2 E:ASP194 4.0 12.1 1.0
N E:GLN64 4.0 10.4 1.0
O E:ALA195 4.1 14.6 1.0
CA E:GLN64 4.2 10.4 1.0
O E:ASP194 4.2 12.1 1.0
C E:ASP194 4.2 12.1 1.0
CA E:ASP194 4.3 12.1 1.0
N E:SER61 4.3 11.9 1.0
CA E:SER61 4.3 11.9 1.0
CG f:GLU25 4.3 12.4 1.0
OE2 f:GLU25 4.4 12.4 1.0
CB E:ASP194 4.4 12.1 1.0
N E:GLY62 4.4 11.7 1.0
CB E:GLN64 4.4 10.4 1.0
CB E:SER61 4.5 11.9 1.0
CA E:GLY62 4.5 11.7 1.0
N E:VAL65 4.6 9.1 1.0
C E:GLY62 4.7 11.7 1.0
N E:ASP63 4.8 10.7 1.0
N E:ALA195 4.8 14.6 1.0
CG1 E:VAL65 4.8 9.1 1.0
CA E:VAL65 4.9 9.1 1.0
C E:ALA195 4.9 14.6 1.0

Calcium binding site 9 out of 92 in 8qkm

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Calcium binding site 9 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca202

b:23.4
occ:1.00
 OD1 l:ASP55 2.4 13.5 1.0
OD1 E:ASP55 2.4 13.3 1.0
OD1 f:ASP55 2.4 13.4 1.0
CG E:ASP55 3.6 13.3 1.0
CG l:ASP55 3.6 13.5 1.0
CG f:ASP55 3.6 13.4 1.0
OG E:SER61 4.3 11.9 1.0
OG f:SER61 4.3 12.0 1.0
OG l:SER61 4.3 12.0 1.0
OD2 E:ASP55 4.3 13.3 1.0
OD2 l:ASP55 4.3 13.5 1.0
OD2 f:ASP55 4.3 13.4 1.0
O f:GLY54 4.4 12.7 1.0
O l:GLY54 4.4 12.6 1.0
O E:GLY54 4.4 12.4 1.0
CB f:SER61 4.4 12.0 1.0
CB E:SER61 4.4 11.9 1.0
CB l:SER61 4.4 12.0 1.0
CB f:ASP55 4.7 13.4 1.0
CB l:ASP55 4.7 13.5 1.0
CB E:ASP55 4.7 13.3 1.0
CA f:ASP55 4.8 13.4 1.0
CA l:ASP55 4.8 13.5 1.0
CA E:ASP55 4.8 13.3 1.0
C f:GLY54 5.0 12.7 1.0
C l:GLY54 5.0 12.6 1.0
C E:GLY54 5.0 12.4 1.0

Calcium binding site 10 out of 92 in 8qkm

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Calcium binding site 10 out of 92 in the Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Symmetric Structure of Satellite Tobacco Necrosis Virus-Like Particle with PS1-5 Grna within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:10.9
occ:1.00
 OD1 F:ASP194 2.3 12.2 1.0
OE1 y:GLU25 2.4 12.9 1.0
O F:SER61 2.4 12.2 1.0
O F:GLN64 2.4 10.9 1.0
CG F:ASP194 3.2 12.2 1.0
C F:GLN64 3.5 10.9 1.0
C F:SER61 3.5 12.2 1.0
CD y:GLU25 3.6 12.9 1.0
OD2 F:ASP194 3.8 12.2 1.0
CB y:GLU25 4.0 12.9 1.0
O F:ASP194 4.0 12.2 1.0
C F:ASP194 4.0 12.2 1.0
CA F:ASP194 4.0 12.2 1.0
CB F:ASP194 4.2 12.2 1.0
N F:GLN64 4.2 10.9 1.0
N F:SER61 4.3 12.2 1.0
CA F:SER61 4.3 12.2 1.0
CA F:GLN64 4.3 10.9 1.0
CG y:GLU25 4.4 12.9 1.0
CB F:SER61 4.4 12.2 1.0
O F:ALA195 4.4 14.8 1.0
OE2 y:GLU25 4.5 12.9 1.0
CB F:GLN64 4.5 10.9 1.0
N F:VAL65 4.5 9.0 1.0
N F:GLY62 4.6 12.2 1.0
N F:ALA195 4.7 14.8 1.0
CA F:GLY62 4.7 12.2 1.0
CA F:VAL65 4.7 9.0 1.0
C F:ALA195 4.8 14.8 1.0
CG1 F:VAL65 4.9 9.0 1.0
C F:GLY62 4.9 12.2 1.0

Reference:

E.Wroblewski, A.Javed, P.C.Mata, N.Patel, G.Leonov, V.E.S.Philips, R.Twarock, G.P.Stockley. Virion Assembly Is Regulated By Sequence-Specific and Flexible Genomic Rna-Coat Protein Contacts To Be Published.
Page generated: Thu Jul 10 06:35:00 2025

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