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Zinc in PDB 2w0d: Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.

Enzymatic activity of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.

All present enzymatic activity of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.:
3.4.24.65;

Protein crystallography data

The structure of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases., PDB code: 2w0d was solved by J.Isaksson, S.Nystrom, D.J.Derbyshire, H.Wallberg, T.Agback, H.Kovacs, I.Bertini, I.C.Felli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.71 / 2.00
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 38.160, 99.939, 79.423, 90.00, 96.59, 90.00
R / Rfree (%) 17.9 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. (pdb code 2w0d). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases., PDB code: 2w0d:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 1 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1264

b:6.0
occ:1.00
NE2 A:HIS218 2.1 5.1 1.0
O47 A:CGS1273 2.1 5.6 1.0
NE2 A:HIS228 2.1 4.6 1.0
O48 A:CGS1273 2.2 5.8 1.0
NE2 A:HIS222 2.2 5.0 1.0
C34 A:CGS1273 2.8 5.3 1.0
N35 A:CGS1273 2.9 4.8 1.0
CD2 A:HIS218 3.0 5.0 1.0
CD2 A:HIS228 3.1 4.5 1.0
CD2 A:HIS222 3.1 5.2 1.0
CE1 A:HIS228 3.1 4.9 1.0
CE1 A:HIS218 3.1 4.9 1.0
CE1 A:HIS222 3.2 4.8 1.0
O A:HOH2195 3.9 2.0 1.0
CG A:HIS218 4.1 5.0 1.0
ND1 A:HIS218 4.2 4.8 1.0
ND1 A:HIS228 4.2 4.6 1.0
CG A:HIS228 4.2 5.0 1.0
CA A:CGS1273 4.3 5.2 1.0
CG A:HIS222 4.3 5.1 1.0
ND1 A:HIS222 4.3 5.3 1.0
O A:HOH2196 4.4 3.9 1.0
CG1 A:CGS1273 4.8 5.1 1.0
N1 A:CGS1273 4.8 5.5 1.0
CE1 A:CGS1273 4.9 4.5 1.0
CE A:MET236 4.9 3.3 1.0
CB A:CGS1273 4.9 4.5 1.0
CC A:CGS1273 4.9 5.5 1.0

Zinc binding site 2 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 2 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1265

b:5.5
occ:1.00
OD1 A:ASP170 1.9 4.9 1.0
NE2 A:HIS183 1.9 2.8 1.0
NE2 A:HIS168 2.1 5.1 1.0
ND1 A:HIS196 2.1 3.6 1.0
CG A:ASP170 2.9 4.4 1.0
CE1 A:HIS183 2.9 4.6 1.0
CD2 A:HIS168 3.0 5.0 1.0
CD2 A:HIS183 3.0 3.3 1.0
CG A:HIS196 3.1 5.2 1.0
CE1 A:HIS196 3.1 4.8 1.0
CE1 A:HIS168 3.1 5.0 1.0
OD2 A:ASP170 3.2 4.0 1.0
CB A:HIS196 3.4 5.1 1.0
ND1 A:HIS183 4.0 3.6 1.0
CG A:HIS183 4.1 4.4 1.0
CG A:HIS168 4.1 5.0 1.0
ND1 A:HIS168 4.2 4.6 1.0
NE2 A:HIS196 4.2 5.5 1.0
CD2 A:HIS196 4.2 4.9 1.0
CB A:ASP170 4.2 4.6 1.0
CE1 A:PHE185 4.4 5.8 1.0
O A:HIS172 4.4 4.7 1.0
CZ A:PHE174 4.5 4.9 1.0
CE2 A:PHE174 4.7 4.8 1.0
CZ A:PHE185 4.7 5.8 1.0
CB A:HIS172 4.8 4.5 1.0
CA A:HIS196 4.9 4.9 1.0

Zinc binding site 3 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 3 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1269

b:3.4
occ:1.00
OXT A:ACT1270 1.9 3.0 1.0
NE2 D:HIS172 2.0 2.2 1.0
NE2 A:HIS172 2.1 6.1 1.0
O A:ACT1271 2.1 7.7 1.0
C A:ACT1270 2.9 3.4 1.0
CD2 D:HIS172 2.9 4.3 1.0
C A:ACT1271 3.0 8.0 1.0
CD2 A:HIS172 3.0 6.4 1.0
O A:ACT1270 3.0 3.3 1.0
OXT A:ACT1271 3.0 8.0 1.0
CE1 A:HIS172 3.1 6.0 1.0
CE1 D:HIS172 3.1 3.7 1.0
CG D:HIS172 4.1 4.3 1.0
O D:HOH2075 4.2 4.9 1.0
ND1 D:HIS172 4.2 5.9 1.0
ND1 A:HIS172 4.2 7.3 1.0
CG A:HIS172 4.2 6.0 1.0
O A:HOH2193 4.2 17.7 1.0
CH3 A:ACT1270 4.2 3.0 1.0
CH3 A:ACT1271 4.4 8.3 1.0
CE2 A:PHE185 4.5 6.7 1.0
O D:ASP170 4.5 4.8 1.0
CB A:PHE171 4.7 3.6 1.0
O A:HOH2194 4.9 10.6 1.0

Zinc binding site 4 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 4 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1264

b:6.6
occ:1.00
NE2 B:HIS218 2.1 5.2 1.0
O47 B:CGS1269 2.1 4.9 1.0
NE2 B:HIS228 2.1 4.8 1.0
NE2 B:HIS222 2.2 5.1 1.0
O48 B:CGS1269 2.2 6.0 1.0
C34 B:CGS1269 2.9 5.3 1.0
CD2 B:HIS218 2.9 4.8 1.0
N35 B:CGS1269 3.0 4.8 1.0
CD2 B:HIS228 3.1 4.5 1.0
CD2 B:HIS222 3.1 5.2 1.0
CE1 B:HIS218 3.1 4.8 1.0
CE1 B:HIS228 3.1 4.8 1.0
CE1 B:HIS222 3.2 4.6 1.0
O B:HOH2169 4.0 2.0 1.0
CG B:HIS218 4.1 5.2 1.0
ND1 B:HIS218 4.2 4.4 1.0
ND1 B:HIS228 4.2 4.6 1.0
CG B:HIS228 4.2 5.1 1.0
CG B:HIS222 4.3 5.4 1.0
ND1 B:HIS222 4.3 4.9 1.0
CA B:CGS1269 4.3 4.7 1.0
O B:HOH2168 4.5 2.0 1.0
N1 B:CGS1269 4.8 4.5 1.0
CE B:MET236 4.9 2.6 1.0
CG1 B:CGS1269 4.9 4.8 1.0
CE1 B:CGS1269 4.9 3.2 1.0
CC B:CGS1269 5.0 4.5 1.0

Zinc binding site 5 out of 10 in 2w0d

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Zinc binding site 5 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1265

b:5.5
occ:1.00
OD1 B:ASP170 1.9 5.3 1.0
NE2 B:HIS183 2.0 3.9 1.0
ND1 B:HIS196 2.0 4.7 1.0
NE2 B:HIS168 2.1 5.2 1.0
CG B:ASP170 2.9 5.2 1.0
CE1 B:HIS196 2.9 3.8 1.0
CE1 B:HIS183 2.9 5.9 1.0
CD2 B:HIS168 3.0 4.9 1.0
CD2 B:HIS183 3.1 4.2 1.0
CG B:HIS196 3.1 3.7 1.0
CE1 B:HIS168 3.1 5.0 1.0
OD2 B:ASP170 3.1 6.0 1.0
CB B:HIS196 3.5 4.8 1.0
NE2 B:HIS196 4.1 2.0 1.0
ND1 B:HIS183 4.1 4.5 1.0
CG B:HIS168 4.1 5.0 1.0
CG B:HIS183 4.2 5.2 1.0
ND1 B:HIS168 4.2 4.8 1.0
CD2 B:HIS196 4.2 4.1 1.0
O B:HIS172 4.2 4.9 1.0
CB B:ASP170 4.2 4.9 1.0
CE1 B:PHE185 4.4 4.3 1.0
CZ B:PHE174 4.6 5.0 1.0
CE2 B:PHE174 4.8 4.7 1.0
CZ B:PHE185 4.8 4.4 1.0
CB B:HIS172 4.9 4.5 1.0
O B:HOH2072 4.9 2.0 1.0

Zinc binding site 6 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 6 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1264

b:5.9
occ:1.00
NE2 C:HIS218 2.1 5.1 1.0
NE2 C:HIS228 2.1 4.6 1.0
O47 C:CGS1273 2.1 4.5 1.0
NE2 C:HIS222 2.2 4.8 1.0
O48 C:CGS1273 2.2 4.7 1.0
C34 C:CGS1273 2.9 4.7 1.0
N35 C:CGS1273 2.9 3.6 1.0
CD2 C:HIS218 3.0 5.0 1.0
CD2 C:HIS228 3.0 4.5 1.0
CE1 C:HIS228 3.1 4.9 1.0
CE1 C:HIS218 3.1 4.9 1.0
CD2 C:HIS222 3.1 5.0 1.0
CE1 C:HIS222 3.2 4.8 1.0
O C:HOH2143 4.1 2.0 1.0
CG C:HIS218 4.2 5.0 1.0
ND1 C:HIS218 4.2 4.8 1.0
CG C:HIS228 4.2 5.2 1.0
ND1 C:HIS228 4.2 4.6 1.0
ND1 C:HIS222 4.3 5.0 1.0
CG C:HIS222 4.3 5.5 1.0
CA C:CGS1273 4.3 5.3 1.0
O C:HOH2145 4.4 4.1 1.0
O C:HOH2098 4.7 5.8 1.0
N1 C:CGS1273 4.9 5.0 1.0
CE C:MET236 4.9 3.6 1.0
CC C:CGS1273 5.0 5.2 1.0
CE1 C:CGS1273 5.0 5.0 1.0
CB C:PRO238 5.0 4.8 1.0
CG1 C:CGS1273 5.0 4.5 1.0

Zinc binding site 7 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 7 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1265

b:6.5
occ:1.00
OD1 C:ASP170 2.0 4.9 1.0
NE2 C:HIS168 2.1 5.2 1.0
NE2 C:HIS183 2.1 5.0 1.0
ND1 C:HIS196 2.1 2.9 1.0
CG C:ASP170 2.9 4.5 1.0
CD2 C:HIS168 3.0 5.1 1.0
CE1 C:HIS196 3.0 4.7 1.0
CE1 C:HIS183 3.1 3.9 1.0
CD2 C:HIS183 3.1 3.1 1.0
CE1 C:HIS168 3.1 5.1 1.0
OD2 C:ASP170 3.2 2.9 1.0
CG C:HIS196 3.2 4.3 1.0
CB C:HIS196 3.5 4.9 1.0
O C:HIS172 4.1 4.5 1.0
CG C:HIS168 4.2 5.0 1.0
NE2 C:HIS196 4.2 3.3 1.0
ND1 C:HIS168 4.2 4.7 1.0
ND1 C:HIS183 4.2 4.5 1.0
CG C:HIS183 4.2 4.8 1.0
CD2 C:HIS196 4.3 2.8 1.0
CB C:ASP170 4.3 3.8 1.0
CE1 C:PHE185 4.4 5.5 1.0
CZ C:PHE174 4.6 5.2 1.0
CZ C:PHE185 4.7 4.7 1.0
O C:HOH2060 4.8 2.0 1.0
CE2 C:PHE174 4.8 4.8 1.0

Zinc binding site 8 out of 10 in 2w0d

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Zinc binding site 8 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1269

b:3.9
occ:1.00
OXT C:ACT1270 1.8 2.5 1.0
NE2 C:HIS172 2.0 5.7 1.0
OXT C:ACT1272 2.1 11.9 1.0
C C:ACT1270 2.8 2.5 1.0
O C:ACT1272 2.9 13.2 1.0
C C:ACT1272 2.9 12.7 1.0
CE1 C:HIS172 3.0 5.5 1.0
O C:ACT1270 3.0 2.6 1.0
CD2 C:HIS172 3.1 5.8 1.0
O C:HOH2141 3.9 9.2 1.0
O C:HOH2061 4.1 6.5 1.0
ND1 C:HIS172 4.1 6.4 1.0
CH3 C:ACT1270 4.2 2.5 1.0
CG C:HIS172 4.2 5.4 1.0
CH3 C:ACT1272 4.4 12.6 1.0
O C:ASP170 4.6 4.5 1.0

Zinc binding site 9 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 9 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1264

b:6.0
occ:1.00
NE2 D:HIS228 2.0 4.7 1.0
O47 D:CGS1273 2.1 4.6 1.0
NE2 D:HIS218 2.1 5.2 1.0
NE2 D:HIS222 2.2 5.0 1.0
O48 D:CGS1273 2.2 4.6 1.0
C34 D:CGS1273 2.8 5.3 1.0
N35 D:CGS1273 2.9 4.7 1.0
CD2 D:HIS228 2.9 4.5 1.0
CE1 D:HIS228 3.0 4.8 1.0
CD2 D:HIS218 3.0 4.9 1.0
CD2 D:HIS222 3.1 5.1 1.0
CE1 D:HIS222 3.1 5.0 1.0
CE1 D:HIS218 3.1 5.0 1.0
O D:HOH2171 4.1 2.0 1.0
ND1 D:HIS228 4.1 4.6 1.0
CG D:HIS228 4.1 5.2 1.0
CG D:HIS218 4.2 5.1 1.0
ND1 D:HIS218 4.2 4.8 1.0
ND1 D:HIS222 4.2 5.0 1.0
CG D:HIS222 4.3 5.2 1.0
CA D:CGS1273 4.3 5.0 1.0
O D:HOH2170 4.4 9.1 1.0
CE D:MET236 4.8 3.4 1.0
N1 D:CGS1273 4.9 6.0 1.0
O D:HOH2119 4.9 9.1 1.0
CC D:CGS1273 5.0 5.9 1.0

Zinc binding site 10 out of 10 in 2w0d

Go back to Zinc Binding Sites List in 2w0d
Zinc binding site 10 out of 10 in the Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1265

b:5.8
occ:1.00
OD1 D:ASP170 1.9 5.7 1.0
NE2 D:HIS168 1.9 5.0 1.0
NE2 D:HIS183 2.1 5.8 1.0
ND1 D:HIS196 2.2 4.1 1.0
CD2 D:HIS168 2.8 4.9 1.0
CG D:ASP170 2.9 5.9 1.0
CE1 D:HIS183 3.0 6.3 1.0
CE1 D:HIS168 3.0 5.1 1.0
CE1 D:HIS196 3.1 5.8 1.0
CD2 D:HIS183 3.2 5.0 1.0
CG D:HIS196 3.2 4.7 1.0
OD2 D:ASP170 3.3 4.6 1.0
CB D:HIS196 3.5 4.3 1.0
CG D:HIS168 4.0 5.2 1.0
O D:HIS172 4.0 5.5 1.0
ND1 D:HIS168 4.0 4.8 1.0
ND1 D:HIS183 4.1 5.4 1.0
CB D:ASP170 4.2 4.8 1.0
NE2 D:HIS196 4.2 5.7 1.0
CG D:HIS183 4.3 5.2 1.0
CD2 D:HIS196 4.3 4.7 1.0
CE1 D:PHE185 4.5 5.2 1.0
CZ D:PHE174 4.6 5.2 1.0
CE2 D:PHE174 4.7 4.8 1.0
CZ D:PHE185 4.7 6.1 1.0
O D:HOH2073 4.9 2.0 1.0
CE2 A:PHE171 5.0 3.2 1.0

Reference:

J.Isaksson, S.Nystrom, D.J.Derbyshire, H.Wallberg, T.Agback, H.Kovacs, I.Bertini, I.C.Felli. Does A Fast Nuclear Magnetic Resonance Spectroscopy- and X-Ray Crystallography Hybrid Approach Provide Reliable Structural Information of Ligand-Protein Complexes? A Case Study of Metalloproteinases. J.Med.Chem. V. 52 1712 2009.
ISSN: ISSN 0022-2623
PubMed: 19239231
DOI: 10.1021/JM801388Q
Page generated: Sat Sep 26 04:16:13 2020
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