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Potassium in PDB 7p2t: Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative

Protein crystallography data

The structure of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative, PDB code: 7p2t was solved by F.Saccoccia, S.Gemma, G.Campiani, G.Ruberti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.06 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 99.205, 99.003, 178.585, 90, 91.3, 90
R / Rfree (%) n/a / 29.4

Other elements in 7p2t:

The structure of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom
Bromine (Br) 4 atoms

Potassium Binding Sites:

The binding sites of Potassium atom in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative (pdb code 7p2t). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative, PDB code: 7p2t:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 1 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K502

b:42.9
occ:1.00
 OG A:SER207 2.7 44.7 1.0
O A:ASP186 2.7 40.3 1.0
OD1 A:ASP184 2.8 42.4 1.0
O A:VAL208 2.8 42.2 1.0
O A:HIS188 2.8 38.1 1.0
O A:ASP184 3.3 41.9 1.0
CG A:ASP184 3.4 42.3 1.0
N A:ASP186 3.4 40.8 1.0
C A:VAL208 3.6 42.0 1.0
C A:ASP186 3.6 40.3 1.0
C A:ASP184 3.6 41.9 1.0
CB A:ASP184 3.7 42.2 1.0
N A:VAL208 3.7 43.1 1.0
CB A:HIS209 3.9 41.0 1.0
C A:HIS188 3.9 39.0 1.0
CA A:ASP186 3.9 40.4 1.0
CB A:SER207 4.0 44.5 1.0
C A:LEU185 4.0 41.3 1.0
N A:LEU185 4.1 41.6 1.0
ND1 A:HIS209 4.1 41.2 1.0
CB A:ASP186 4.1 40.1 1.0
CA A:ASP184 4.3 42.1 1.0
CA A:HIS189 4.3 38.6 1.0
CA A:VAL208 4.3 42.5 1.0
N A:GLY190 4.3 39.1 1.0
CA A:SER207 4.3 44.3 1.0
CA A:HIS209 4.3 41.1 1.0
N A:HIS209 4.3 41.6 1.0
CA A:LEU185 4.3 41.4 1.0
OD2 A:ASP184 4.4 42.8 1.0
C A:SER207 4.4 43.9 1.0
CG A:HIS209 4.4 41.1 1.0
N A:HIS189 4.5 38.7 1.0
CE1 A:HIS141 4.6 39.3 1.0
C A:HIS189 4.6 38.9 1.0
N A:HIS188 4.7 39.8 1.0
N A:LEU187 4.8 40.2 1.0
O A:LEU185 4.8 41.6 1.0
C A:LEU187 4.9 40.0 1.0
CG1 A:VAL208 4.9 42.1 1.0
CA A:HIS188 5.0 39.3 1.0

Potassium binding site 2 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 2 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K503

b:58.0
occ:1.00
 O A:PHE197 2.8 49.0 1.0
OG A:SER243 2.8 46.1 1.0
O A:VAL203 3.1 49.4 1.0
O A:SER200 3.4 48.9 1.0
CB A:SER243 3.7 45.8 1.0
C A:PHE197 3.9 48.7 1.0
O A:SER243 3.9 45.6 1.0
C A:SER243 4.0 45.8 1.0
N A:THR205 4.0 47.8 1.0
OG1 A:THR205 4.1 46.7 1.0
CB A:PHE197 4.2 48.9 1.0
C A:VAL203 4.3 49.2 1.0
CB A:THR205 4.3 47.0 1.0
N A:ALA244 4.3 46.0 1.0
CA A:VAL204 4.5 48.8 1.0
CA A:SER243 4.5 45.8 1.0
C A:SER200 4.6 48.5 1.0
CA A:ALA244 4.6 46.1 1.0
CA A:PHE197 4.7 48.7 1.0
O A:GLY240 4.7 43.8 1.0
CB A:ALA244 4.7 46.1 1.0
C A:VAL204 4.7 48.5 1.0
N A:TRP198 4.8 48.5 1.0
CA A:THR205 4.8 47.2 1.0
CA A:TRP198 4.8 48.2 1.0
O A:TRP198 4.8 47.6 1.0
N A:VAL204 4.9 49.1 1.0
C A:TRP198 4.9 48.1 1.0

Potassium binding site 3 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 3 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K502

b:44.3
occ:1.00
 OG B:SER207 2.8 40.6 1.0
O B:ASP186 2.8 39.6 1.0
O B:HIS188 2.9 42.5 1.0
O B:VAL208 3.0 41.2 1.0
OD1 B:ASP184 3.0 37.7 1.0
CG B:ASP184 3.2 37.8 1.0
O B:ASP184 3.3 38.1 1.0
N B:ASP186 3.3 38.4 1.0
CB B:ASP184 3.5 38.0 1.0
C B:ASP184 3.5 38.0 1.0
C B:ASP186 3.6 39.3 1.0
C B:VAL208 3.8 41.0 1.0
CA B:ASP186 3.8 38.9 1.0
N B:VAL208 3.9 40.9 1.0
OD2 B:ASP184 3.9 37.7 1.0
N B:LEU185 3.9 37.6 1.0
C B:LEU185 3.9 38.0 1.0
CB B:ASP186 4.0 39.0 1.0
C B:HIS188 4.0 42.4 1.0
CB B:SER207 4.0 41.0 1.0
CA B:ASP184 4.1 38.0 1.0
CB B:HIS209 4.1 40.7 1.0
CA B:LEU185 4.2 37.8 1.0
ND1 B:HIS209 4.3 40.5 1.0
N B:GLY190 4.4 42.4 1.0
CA B:SER207 4.4 41.0 1.0
CA B:HIS189 4.5 42.1 1.0
CA B:VAL208 4.5 41.0 1.0
CA B:HIS209 4.5 40.8 1.0
C B:SER207 4.6 41.0 1.0
N B:HIS209 4.6 40.9 1.0
CG B:HIS209 4.7 40.6 1.0
C B:HIS189 4.7 42.2 1.0
N B:HIS189 4.7 42.3 1.0
N B:LEU187 4.8 39.7 1.0
O B:LEU185 4.8 38.1 1.0
N B:HIS188 4.8 41.8 1.0
NE2 B:HIS141 4.9 35.2 1.0
C B:LEU187 4.9 40.9 1.0

Potassium binding site 4 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 4 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K503

b:73.4
occ:1.00
 O B:PHE197 2.8 45.1 1.0
OG B:SER243 2.8 47.0 1.0
O B:VAL203 2.9 44.1 1.0
O B:SER200 3.4 45.4 1.0
O B:SER243 3.5 46.6 1.0
CB B:SER243 3.8 47.1 1.0
OG1 B:THR205 3.8 42.4 1.0
C B:PHE197 3.9 44.9 1.0
C B:SER243 4.0 46.8 1.0
C B:VAL203 4.1 43.8 1.0
N B:THR205 4.3 42.5 1.0
CB B:PHE197 4.3 45.6 1.0
CA B:VAL204 4.5 43.0 1.0
CG2 B:THR205 4.5 42.3 1.0
O B:TRP198 4.5 45.0 1.0
CA B:SER243 4.5 47.1 1.0
C B:SER200 4.6 44.9 1.0
N B:ALA244 4.6 46.6 1.0
O B:GLY240 4.6 48.4 1.0
CB B:THR205 4.7 42.3 1.0
CA B:TRP198 4.7 44.6 1.0
N B:TRP198 4.7 44.9 1.0
N B:VAL204 4.7 43.4 1.0
C B:TRP198 4.8 44.7 1.0
CB B:ALA244 4.8 46.6 1.0
CA B:PHE197 4.8 45.4 1.0
CA B:ALA244 4.8 46.8 1.0
C B:VAL204 4.9 43.0 1.0

Potassium binding site 5 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 5 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K504

b:119.9
occ:1.00
 OE1 B:GLU80 2.9 58.9 1.0
CD B:GLU80 3.2 58.9 1.0
CB B:GLU80 3.5 58.6 1.0
OE2 B:GLU80 3.6 58.7 1.0
CG B:GLU80 3.9 58.8 1.0
CD2 B:LEU77 4.0 55.4 1.0
CA B:GLU80 4.9 58.6 1.0
CA B:LEU77 5.0 55.8 1.0

Potassium binding site 6 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 6 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K502

b:52.1
occ:1.00
 O C:ASP186 2.7 47.4 1.0
OG C:SER207 2.8 47.3 1.0
O C:VAL208 2.9 46.4 1.0
O C:HIS188 2.9 47.0 1.0
OD1 C:ASP184 3.1 46.8 1.0
CG C:ASP184 3.3 46.6 1.0
O C:ASP184 3.4 46.4 1.0
N C:ASP186 3.6 46.8 1.0
C C:ASP186 3.6 47.2 1.0
CB C:ASP184 3.6 46.5 1.0
C C:ASP184 3.7 46.5 1.0
C C:VAL208 3.7 46.2 1.0
C C:HIS188 3.9 47.0 1.0
N C:VAL208 3.9 46.7 1.0
OD2 C:ASP184 4.0 46.6 1.0
CA C:ASP186 4.0 46.9 1.0
CB C:HIS209 4.0 46.3 1.0
CB C:SER207 4.1 47.4 1.0
C C:LEU185 4.1 46.6 1.0
N C:LEU185 4.2 46.2 1.0
CB C:ASP186 4.2 46.9 1.0
CA C:HIS189 4.2 46.6 1.0
N C:GLY190 4.3 46.9 1.0
CA C:ASP184 4.3 46.5 1.0
ND1 C:HIS209 4.4 46.6 1.0
CA C:HIS209 4.4 46.3 1.0
CA C:SER207 4.5 47.3 1.0
C C:SER207 4.5 47.0 1.0
N C:HIS189 4.5 46.7 1.0
N C:HIS209 4.5 46.2 1.0
CA C:LEU185 4.5 46.4 1.0
CA C:VAL208 4.5 46.3 1.0
CE1 C:HIS141 4.6 49.8 1.0
CG C:HIS209 4.6 46.6 1.0
C C:HIS189 4.6 46.8 1.0
N C:HIS188 4.7 47.5 1.0
C C:LEU187 4.8 47.3 1.0
N C:LEU187 4.8 47.2 1.0
O C:LEU185 4.9 47.0 1.0
O C:LEU187 4.9 47.7 1.0
CA C:HIS188 5.0 47.1 1.0

Potassium binding site 7 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 7 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K503

b:59.9
occ:1.00
 O C:PHE197 2.8 49.9 1.0
O C:VAL203 3.1 51.2 1.0
O C:SER200 3.4 51.7 1.0
CB C:SER243 3.6 57.0 1.0
O C:SER243 3.8 56.7 1.0
C C:PHE197 3.9 50.0 1.0
C C:SER243 3.9 57.2 1.0
OG1 C:THR205 4.0 50.4 1.0
CG2 C:THR205 4.0 50.0 1.0
N C:THR205 4.2 50.5 1.0
C C:VAL203 4.3 51.1 1.0
N C:ALA244 4.3 57.2 1.0
CB C:PHE197 4.3 50.2 1.0
CA C:SER243 4.5 57.1 1.0
CB C:THR205 4.5 50.0 1.0
CA C:ALA244 4.5 57.0 1.0
CA C:VAL204 4.5 50.8 1.0
C C:SER200 4.6 51.0 1.0
CB C:ALA244 4.6 57.1 1.0
O C:TRP198 4.6 50.0 1.0
OG C:SER243 4.7 57.6 1.0
CA C:PHE197 4.8 50.2 1.0
O C:GLY240 4.8 56.2 1.0
N C:TRP198 4.8 50.0 1.0
CA C:TRP198 4.8 50.0 1.0
C C:VAL204 4.9 50.7 1.0
C C:TRP198 4.9 50.0 1.0
N C:VAL204 4.9 51.0 1.0

Potassium binding site 8 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 8 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:

Potassium binding site 9 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 9 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K502

b:59.5
occ:1.00
 O D:VAL208 2.8 52.3 1.0
O D:HIS188 2.9 50.0 1.0
O D:ASP186 2.9 51.9 1.0
O D:ASP184 3.0 51.4 1.0
OD1 D:ASP184 3.2 50.9 1.0
CG D:ASP184 3.4 51.0 1.0
C D:ASP184 3.6 51.0 1.0
CB D:ASP184 3.6 51.0 1.0
N D:ASP186 3.6 51.0 1.0
C D:VAL208 3.7 52.0 1.0
C D:ASP186 3.7 51.7 1.0
N D:VAL208 3.8 51.5 1.0
CB D:SER207 3.9 50.7 1.0
C D:HIS188 3.9 50.2 1.0
CB D:HIS209 3.9 52.5 1.0
ND1 D:HIS209 3.9 52.4 1.0
CA D:ASP186 4.0 51.4 1.0
N D:GLY190 4.1 49.0 1.0
OD2 D:ASP184 4.1 50.8 1.0
CA D:ASP184 4.2 51.1 1.0
CB D:ASP186 4.2 51.4 1.0
CA D:HIS189 4.2 49.3 1.0
CA D:SER207 4.3 50.8 1.0
C D:LEU185 4.3 50.9 1.0
C D:SER207 4.3 51.1 1.0
N D:LEU185 4.3 50.7 1.0
CG D:HIS209 4.3 52.4 1.0
N D:HIS209 4.4 52.3 1.0
CA D:VAL208 4.4 51.5 1.0
CA D:HIS209 4.4 52.4 1.0
C D:HIS189 4.5 49.3 1.0
OG D:SER207 4.5 50.2 1.0
N D:HIS189 4.5 49.7 1.0
CA D:LEU185 4.6 50.7 1.0
O D:HOH603 4.7 38.8 1.0
N D:HIS188 4.8 51.1 1.0
N D:LEU187 4.9 51.7 1.0
C D:LEU187 4.9 51.5 1.0
CA D:GLY190 4.9 48.8 1.0
NE2 D:HIS141 5.0 47.4 1.0

Potassium binding site 10 out of 10 in 7p2t

Go back to Potassium Binding Sites List in 7p2t
Potassium binding site 10 out of 10 in the Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Tetartohedrally Twinned Crystal Structure of Schistosoma Mansoni HDAC8 in Complex with A Tricyclic Thieno[3,2-B]Indole Capped Hydroxamate- Based Inhibitor, Bromine Derivative within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K503

b:67.0
occ:1.00
 O D:PHE197 2.8 49.4 1.0
O D:VAL203 2.8 51.7 1.0
O D:SER243 2.9 43.1 1.0
OG D:SER243 2.9 42.7 1.0
O D:SER200 3.3 48.8 1.0
CB D:SER243 3.8 43.0 1.0
C D:SER243 3.8 43.4 1.0
C D:PHE197 3.9 49.3 1.0
C D:VAL203 4.0 51.5 1.0
N D:THR205 4.1 51.6 1.0
CB D:PHE197 4.2 49.3 1.0
CA D:VAL204 4.3 51.7 1.0
OG1 D:THR205 4.4 51.1 1.0
C D:SER200 4.5 48.9 1.0
CA D:SER243 4.5 43.1 1.0
CB D:THR205 4.6 51.2 1.0
N D:VAL204 4.6 51.5 1.0
CA D:PHE197 4.7 49.3 1.0
C D:VAL204 4.7 51.8 1.0
N D:TRP198 4.8 49.1 1.0
N D:ALA244 4.8 43.8 1.0
O D:GLY240 4.8 43.9 1.0
CA D:TRP198 4.8 49.1 1.0
CA D:THR205 5.0 51.3 1.0
C D:TRP198 5.0 48.7 1.0

Reference:

F.Saccoccia, L.Pozzetti, R.Gimmelli, S.Butini, A.Guidi, G.Papoff, M.Giannaccari, S.Brogi, V.Scognamiglio, S.Gemma, G.Ruberti, G.Campiani. Crystal Structures of Schistosoma Mansoni Histone Deacetylase 8 Reveal A Novel Binding Site For Allosteric Inhibitors. J.Biol.Chem. V. 298 02375 2022.
ISSN: ESSN 1083-351X
PubMed: 35970392
DOI: 10.1016/J.JBC.2022.102375
Page generated: Mon Aug 12 19:49:36 2024

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