Magnesium in PDB 6a2w: Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum

Protein crystallography data

The structure of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum, PDB code: 6a2w was solved by W.Wang, L.J.Yu, T.Y.Kuang, J.R.Shen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.98 / 1.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.749, 115.718, 141.261, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 19.7

Other elements in 6a2w:

The structure of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum (pdb code 6a2w). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum, PDB code: 6a2w:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 6a2w

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Magnesium binding site 1 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:34.8
occ:1.00
MG A:CLA401 0.0 34.8 1.0
ND A:CLA401 2.0 29.6 1.0
NB A:CLA401 2.0 34.0 1.0
NC A:CLA401 2.1 37.2 1.0
NA A:CLA401 2.1 31.9 1.0
O A:HOH517 2.2 34.6 1.0
C4D A:CLA401 2.9 28.6 1.0
C1B A:CLA401 3.0 34.1 1.0
C1C A:CLA401 3.1 37.8 1.0
C4B A:CLA401 3.1 31.5 1.0
C4A A:CLA401 3.1 30.5 1.0
C1A A:CLA401 3.1 29.9 1.0
C4C A:CLA401 3.1 32.6 1.0
C1D A:CLA401 3.2 29.1 1.0
CHC A:CLA401 3.4 35.9 1.0
CHA A:CLA401 3.4 27.9 1.0
CHB A:CLA401 3.4 37.7 1.0
CHD A:CLA401 3.6 28.4 1.0
C3D A:CLA401 4.2 26.1 1.0
C2B A:CLA401 4.3 37.7 1.0
C3B A:CLA401 4.3 35.5 1.0
C2C A:CLA401 4.3 38.7 1.0
O A:PRO10 4.3 39.8 1.0
C3C A:CLA401 4.3 36.2 1.0
C2D A:CLA401 4.3 25.0 1.0
O2 A:A86301 4.4 34.9 1.0
C3A A:CLA401 4.4 30.9 1.0
C2A A:CLA401 4.4 28.4 1.0
NE2 A:GLN9 4.5 35.6 1.0
CD A:PRO11 4.6 40.2 1.0
CBA A:CLA401 4.7 37.0 1.0
CBD A:CLA401 4.9 28.2 1.0
C19 A:A86301 4.9 26.8 1.0

Magnesium binding site 2 out of 9 in 6a2w

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Magnesium binding site 2 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:34.1
occ:1.00
MG A:CLA402 0.0 34.1 1.0
ND A:CLA402 2.0 34.6 1.0
NB A:CLA402 2.0 33.2 1.0
OE2 A:GLU36 2.0 28.5 1.0
NA A:CLA402 2.1 37.3 1.0
NC A:CLA402 2.1 30.0 1.0
C4D A:CLA402 2.9 33.8 1.0
C1B A:CLA402 3.0 33.9 1.0
C4A A:CLA402 3.0 33.1 1.0
CD A:GLU36 3.1 30.0 1.0
C4B A:CLA402 3.1 27.9 1.0
C1C A:CLA402 3.1 26.7 1.0
C1D A:CLA402 3.1 35.6 1.0
C1A A:CLA402 3.1 34.9 1.0
C4C A:CLA402 3.1 28.6 1.0
CHB A:CLA402 3.4 33.0 1.0
CHC A:CLA402 3.4 26.0 1.0
CHA A:CLA402 3.5 34.6 1.0
CHD A:CLA402 3.5 33.5 1.0
O2A A:CLA402 3.8 61.0 1.0
OE1 A:GLU36 3.9 28.7 1.0
CG A:GLU36 3.9 26.1 1.0
C1 A:CLA402 4.0 57.9 1.0
NE A:ARG145 4.1 27.2 1.0
NH2 A:ARG145 4.1 30.1 1.0
C3D A:CLA402 4.2 37.5 1.0
C2B A:CLA402 4.3 31.5 1.0
C3B A:CLA402 4.3 28.1 1.0
C2D A:CLA402 4.3 35.6 1.0
C2C A:CLA402 4.4 25.9 1.0
C3C A:CLA402 4.4 31.3 1.0
C3A A:CLA402 4.4 33.7 1.0
CZ A:ARG145 4.4 28.9 1.0
C2A A:CLA402 4.5 37.5 1.0
C37 A:A86303 4.5 40.7 1.0
O A:HOH505 4.6 56.3 1.0
CGA A:CLA402 4.8 55.9 1.0
CBA A:CLA402 4.9 47.1 1.0
CBD A:CLA402 4.9 37.5 1.0
CB A:GLU36 4.9 26.8 1.0

Magnesium binding site 3 out of 9 in 6a2w

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Magnesium binding site 3 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:30.9
occ:1.00
MG A:KC2403 0.0 30.9 1.0
NC A:KC2403 2.0 29.7 1.0
NB A:KC2403 2.1 31.7 1.0
ND A:KC2403 2.1 29.9 1.0
NA A:KC2403 2.1 32.1 1.0
NE2 A:HIS39 2.2 27.1 1.0
C4D A:KC2403 2.9 29.1 1.0
C4C A:KC2403 3.0 25.9 1.0
C1B A:KC2403 3.0 30.5 1.0
CE1 A:HIS39 3.0 25.1 1.0
C4B A:KC2403 3.1 27.4 1.0
C4A A:KC2403 3.1 31.8 1.0
C1D A:KC2403 3.2 26.4 1.0
C1C A:KC2403 3.2 28.9 1.0
C1A A:KC2403 3.2 30.4 1.0
CD2 A:HIS39 3.3 24.1 1.0
CHD A:KC2403 3.5 26.0 1.0
CHA A:KC2403 3.6 32.8 1.0
CHB A:KC2403 3.6 30.1 1.0
CHC A:KC2403 3.6 27.9 1.0
C9 A:CLA406 3.8 48.4 1.0
C8 A:CLA406 4.0 50.1 1.0
ND1 A:HIS39 4.2 26.1 1.0
C3D A:KC2403 4.2 28.8 1.0
C2B A:KC2403 4.3 30.2 1.0
C3C A:KC2403 4.4 28.7 1.0
C3B A:KC2403 4.4 30.9 1.0
C2D A:KC2403 4.4 28.5 1.0
CG A:HIS39 4.4 22.0 1.0
C3A A:KC2403 4.4 33.0 1.0
C2C A:KC2403 4.4 26.6 1.0
C2A A:KC2403 4.5 32.3 1.0
C10 A:CLA406 4.5 51.4 1.0
CMD A:CLA406 4.7 22.0 1.0
CBD A:KC2403 5.0 38.5 1.0
OBD A:CLA406 5.0 29.1 1.0
CBB A:CLA402 5.0 26.9 1.0

Magnesium binding site 4 out of 9 in 6a2w

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Magnesium binding site 4 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg404

b:21.9
occ:1.00
MG A:CLA404 0.0 21.9 1.0
ND A:CLA404 2.0 22.0 1.0
NB A:CLA404 2.0 20.2 1.0
NC A:CLA404 2.1 20.2 1.0
NA A:CLA404 2.1 21.1 1.0
OE1 A:GLN53 2.1 22.8 1.0
C4D A:CLA404 2.9 22.5 1.0
C1B A:CLA404 3.0 26.9 1.0
C4A A:CLA404 3.0 20.3 1.0
C4B A:CLA404 3.1 18.2 1.0
C4C A:CLA404 3.1 21.6 1.0
C1C A:CLA404 3.1 19.4 1.0
C1D A:CLA404 3.1 26.1 1.0
C1A A:CLA404 3.2 21.2 1.0
CD A:GLN53 3.3 22.5 1.0
CHB A:CLA404 3.4 22.0 1.0
CHA A:CLA404 3.5 24.5 1.0
CHD A:CLA404 3.5 21.9 1.0
CHC A:CLA404 3.5 19.5 1.0
C2 A:CLA404 3.9 26.1 1.0
CG A:GLN53 4.1 20.9 1.0
C3D A:CLA404 4.2 26.3 1.0
O2A A:CLA404 4.2 25.3 1.0
C3 A:CLA404 4.3 26.0 1.0
C2D A:CLA404 4.3 26.1 1.0
NE2 A:GLN53 4.3 22.7 1.0
C1 A:CLA404 4.3 26.3 1.0
C3B A:CLA404 4.3 20.9 1.0
C2B A:CLA404 4.3 22.5 1.0
C3C A:CLA404 4.3 23.1 1.0
C2C A:CLA404 4.4 20.0 1.0
C3A A:CLA404 4.4 22.3 1.0
C2A A:CLA404 4.5 23.3 1.0
C5 A:CLA404 4.7 24.8 1.0
CA A:GLY49 4.7 17.4 1.0
C6 A:CLA404 4.8 24.4 1.0
CBD A:CLA404 4.9 29.6 1.0
CGA A:CLA404 5.0 28.2 1.0
O A:GLY49 5.0 23.7 1.0

Magnesium binding site 5 out of 9 in 6a2w

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Magnesium binding site 5 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg405

b:43.4
occ:1.00
MG A:CLA405 0.0 43.4 1.0
NB A:CLA405 2.0 47.4 1.0
ND A:CLA405 2.0 35.6 1.0
NC A:CLA405 2.1 39.8 1.0
NA A:CLA405 2.1 47.6 1.0
OE1 A:GLN90 2.2 32.4 1.0
C4D A:CLA405 2.9 31.6 1.0
C1B A:CLA405 3.0 50.6 1.0
C4A A:CLA405 3.0 53.1 1.0
C4B A:CLA405 3.1 46.2 1.0
C1C A:CLA405 3.1 41.5 1.0
C1D A:CLA405 3.1 35.8 1.0
C4C A:CLA405 3.1 36.8 1.0
C1A A:CLA405 3.2 45.3 1.0
CD A:GLN90 3.3 33.7 1.0
CHB A:CLA405 3.4 55.7 1.0
CHC A:CLA405 3.4 45.2 1.0
CHA A:CLA405 3.5 38.7 1.0
CHD A:CLA405 3.5 38.3 1.0
NE2 A:GLN90 3.8 33.9 1.0
C28 A:A86302 3.8 36.1 1.0
C3D A:CLA405 4.2 34.2 1.0
C2B A:CLA405 4.3 51.1 1.0
C3B A:CLA405 4.3 50.7 1.0
C2C A:CLA405 4.3 40.2 1.0
C2D A:CLA405 4.3 35.0 1.0
C3C A:CLA405 4.4 40.8 1.0
C3A A:CLA405 4.4 51.5 1.0
C2A A:CLA405 4.5 49.1 1.0
CG A:GLN90 4.6 27.6 1.0
C27 A:A86302 4.7 35.1 1.0
CB A:GLN90 4.9 24.6 1.0
C24 A:DD6308 4.9 73.2 1.0
CBD A:CLA405 4.9 41.1 1.0
C25 A:A86302 5.0 31.3 1.0
C26 A:DD6308 5.0 70.6 1.0

Magnesium binding site 6 out of 9 in 6a2w

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Magnesium binding site 6 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg406

b:26.3
occ:1.00
MG A:CLA406 0.0 26.3 1.0
ND A:CLA406 2.0 23.3 1.0
NB A:CLA406 2.0 20.9 1.0
NA A:CLA406 2.1 23.1 1.0
NC A:CLA406 2.1 26.1 1.0
OE2 A:GLU99 2.1 29.8 1.0
C4D A:CLA406 2.9 27.0 1.0
C1B A:CLA406 3.0 27.8 1.0
C4A A:CLA406 3.1 27.1 1.0
C4B A:CLA406 3.1 23.7 1.0
C1C A:CLA406 3.1 23.5 1.0
C1A A:CLA406 3.1 27.1 1.0
C1D A:CLA406 3.1 21.9 1.0
C4C A:CLA406 3.2 23.5 1.0
CD A:GLU99 3.2 31.1 1.0
CHA A:CLA406 3.4 26.2 1.0
CHB A:CLA406 3.4 29.1 1.0
CHC A:CLA406 3.5 22.8 1.0
CHD A:CLA406 3.5 19.7 1.0
CG A:GLU99 3.8 28.1 1.0
C3D A:CLA406 4.2 24.4 1.0
OE1 A:GLU99 4.2 34.2 1.0
C2B A:CLA406 4.3 28.3 1.0
C2D A:CLA406 4.3 25.3 1.0
C3B A:CLA406 4.3 25.9 1.0
NZ A:LYS38 4.3 22.9 1.0
C2C A:CLA406 4.4 28.7 1.0
C3A A:CLA406 4.4 29.0 1.0
C3C A:CLA406 4.4 22.7 1.0
C2A A:CLA406 4.4 28.7 1.0
CE A:LYS38 4.5 25.8 1.0
CMD A:KC2403 4.6 28.4 1.0
CBD A:CLA406 4.9 25.5 1.0
CB A:GLU99 4.9 25.9 1.0

Magnesium binding site 7 out of 9 in 6a2w

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Magnesium binding site 7 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg407

b:21.7
occ:1.00
MG A:CLA407 0.0 21.7 1.0
ND A:CLA407 2.0 22.0 1.0
NB A:CLA407 2.0 21.5 1.0
NC A:CLA407 2.1 19.9 1.0
NA A:CLA407 2.1 25.1 1.0
OE2 A:GLU140 2.1 21.7 1.0
C4D A:CLA407 2.9 24.3 1.0
C1B A:CLA407 3.0 21.9 1.0
C4B A:CLA407 3.0 20.2 1.0
C4A A:CLA407 3.1 25.6 1.0
C1C A:CLA407 3.1 16.4 1.0
C4C A:CLA407 3.1 21.1 1.0
C1A A:CLA407 3.2 22.7 1.0
C1D A:CLA407 3.2 21.2 1.0
CD A:GLU140 3.2 26.4 1.0
CHB A:CLA407 3.4 23.2 1.0
CHA A:CLA407 3.4 22.2 1.0
CHC A:CLA407 3.4 17.6 1.0
CHD A:CLA407 3.5 20.4 1.0
CG A:GLU140 3.8 21.1 1.0
C26 A:A86304 3.8 26.4 1.0
C29 A:A86304 4.1 26.0 1.0
OE1 A:GLU140 4.2 24.6 1.0
NE A:ARG41 4.2 19.8 1.0
C3D A:CLA407 4.2 22.3 1.0
NH2 A:ARG41 4.3 25.6 1.0
C3B A:CLA407 4.3 15.5 1.0
C2B A:CLA407 4.3 18.1 1.0
C2C A:CLA407 4.3 16.0 1.0
C2D A:CLA407 4.3 20.6 1.0
C3C A:CLA407 4.3 17.9 1.0
C3A A:CLA407 4.4 24.9 1.0
C27 A:A86304 4.4 27.4 1.0
C2A A:CLA407 4.5 23.6 1.0
CB A:GLU140 4.6 24.0 1.0
CZ A:ARG41 4.7 23.9 1.0
C25 A:A86304 4.8 26.2 1.0
C24 A:A86304 4.9 22.7 1.0
CBD A:CLA407 4.9 23.1 1.0
CMA A:CLA407 5.0 27.3 1.0

Magnesium binding site 8 out of 9 in 6a2w

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Magnesium binding site 8 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg408

b:25.0
occ:1.00
MG A:KC1408 0.0 25.0 1.0
NA A:KC1408 2.0 22.0 1.0
NC A:KC1408 2.0 26.6 1.0
NB A:KC1408 2.0 24.2 1.0
ND A:KC1408 2.1 23.9 1.0
OE1 A:GLN143 2.2 23.8 1.0
C4D A:KC1408 2.9 24.2 1.0
C4C A:KC1408 3.0 21.4 1.0
C1B A:KC1408 3.0 24.0 1.0
C4B A:KC1408 3.0 21.9 1.0
C4A A:KC1408 3.0 24.2 1.0
CD A:GLN143 3.1 23.8 1.0
C1A A:KC1408 3.1 20.3 1.0
C1D A:KC1408 3.2 24.9 1.0
C1C A:KC1408 3.2 23.7 1.0
CHA A:KC1408 3.5 23.8 1.0
CHD A:KC1408 3.6 23.5 1.0
NE2 A:GLN143 3.6 24.9 1.0
CHB A:KC1408 3.6 24.1 1.0
CHC A:KC1408 3.6 21.6 1.0
C3D A:KC1408 4.2 22.8 1.0
C3B A:KC1408 4.3 22.8 1.0
C2B A:KC1408 4.3 24.1 1.0
CG A:GLN143 4.3 18.8 1.0
C3A A:KC1408 4.3 23.7 1.0
C3C A:KC1408 4.4 23.6 1.0
C2D A:KC1408 4.4 22.5 1.0
C2A A:KC1408 4.4 26.1 1.0
C2C A:KC1408 4.4 25.9 1.0
C7 A:A86305 4.5 23.8 1.0
CBD A:KC1408 4.9 26.2 1.0

Magnesium binding site 9 out of 9 in 6a2w

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Magnesium binding site 9 out of 9 in the Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Crystal Structure of Fucoxanthin Chlorophyll A/C Complex From Phaeodactylum Tricornutum within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg409

b:41.4
occ:1.00
MG A:CLA409 0.0 41.4 1.0
NB A:CLA409 2.0 36.5 1.0
ND A:CLA409 2.0 47.6 1.0
NC A:CLA409 2.1 37.8 1.0
NA A:CLA409 2.1 46.0 1.0
NE2 A:HIS157 2.2 34.0 1.0
C4D A:CLA409 2.9 50.1 1.0
C1B A:CLA409 3.0 38.8 1.0
C4A A:CLA409 3.1 44.2 1.0
C4B A:CLA409 3.1 35.6 1.0
C1C A:CLA409 3.1 35.5 1.0
CE1 A:HIS157 3.1 36.0 1.0
C4C A:CLA409 3.1 35.3 1.0
C1D A:CLA409 3.1 46.8 1.0
C1A A:CLA409 3.2 51.2 1.0
CD2 A:HIS157 3.3 33.4 1.0
CHB A:CLA409 3.4 41.6 1.0
CHC A:CLA409 3.4 34.9 1.0
CHA A:CLA409 3.5 53.6 1.0
CHD A:CLA409 3.5 44.7 1.0
C4' A:SOG413 4.1 57.6 1.0
C3' A:SOG413 4.2 66.1 1.0
C5' A:SOG413 4.2 53.4 1.0
C3D A:CLA409 4.2 52.2 1.0
ND1 A:HIS157 4.3 32.3 1.0
C2B A:CLA409 4.3 36.6 1.0
C3B A:CLA409 4.3 35.9 1.0
C2C A:CLA409 4.3 34.4 1.0
C2D A:CLA409 4.3 48.6 1.0
C3C A:CLA409 4.4 35.4 1.0
CG A:HIS157 4.4 31.8 1.0
C3A A:CLA409 4.4 50.9 1.0
C2A A:CLA409 4.5 54.5 1.0
C24 A:A86301 4.6 48.1 1.0
C2' A:SOG413 4.9 75.6 1.0
CBD A:CLA409 4.9 58.8 1.0
C2 A:A86301 4.9 44.0 1.0

Reference:

W.Wang, L.J.Yu, C.Xu, T.Tomizaki, S.Zhao, Y.Umena, X.Chen, X.Qin, Y.Xin, M.Suga, G.Han, T.Kuang, J.R.Shen. Structural Basis For Blue-Green Light Harvesting and Energy Dissipation in Diatoms. Science V. 363 2019.
ISSN: ESSN 1095-9203
PubMed: 30733387
DOI: 10.1126/SCIENCE.AAV0365
Page generated: Mon Dec 14 22:18:51 2020

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