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Zinc in PDB 6oad: 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.

Enzymatic activity of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.

All present enzymatic activity of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.:
3.4.11.23;

Protein crystallography data

The structure of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655., PDB code: 6oad was solved by G.Minasov, L.Shuvalova, Z.Wawrzak, O.Kiryukhina, S.Grimshaw, K.Kwon, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.88 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 150.667, 114.761, 161.171, 90.00, 92.02, 90.00
R / Rfree (%) 17.2 / 21.5

Other elements in 6oad:

The structure of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. also contains other interesting chemical elements:

Chlorine (Cl) 11 atoms
Calcium (Ca) 13 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 24;

Binding sites:

The binding sites of Zinc atom in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. (pdb code 6oad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 24 binding sites of Zinc where determined in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655., PDB code: 6oad:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 24 in 6oad

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Zinc binding site 1 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:27.6
occ:1.00
 OD2 A:ASP218 2.0 32.0 1.0
NZ A:LYS195 2.1 32.0 1.0
OE1 A:GLU279 2.1 31.7 1.0
O A:HOH790 2.2 24.0 1.0
CG A:ASP218 2.8 29.4 1.0
OD2 A:ASP200 2.8 32.8 1.0
CE A:LYS195 2.9 29.4 1.0
OD1 A:ASP218 2.9 29.1 1.0
ZN A:ZN502 3.0 27.4 1.0
CD A:GLU279 3.0 29.1 1.0
OE2 A:GLU279 3.3 32.4 1.0
CG A:ASP200 3.6 29.0 1.0
O3 A:BCT505 3.6 28.3 1.0
O A:HOH670 3.9 41.7 1.0
CB A:ASP200 4.0 28.4 1.0
CB A:ASP218 4.2 28.4 1.0
CD A:LYS195 4.3 28.8 1.0
O A:THR304 4.4 26.8 1.0
CG A:GLU279 4.4 27.8 1.0
N A:GLY280 4.4 24.7 1.0
CG1 A:ILE197 4.5 25.6 1.0
O A:ASP277 4.5 31.7 1.0
OD1 A:ASP200 4.6 28.9 1.0
CB A:ILE197 4.6 25.8 1.0
CG2 A:ILE197 4.7 25.6 1.0
CA A:GLY280 4.7 24.7 1.0
C A:BCT505 4.9 32.6 1.0
OD1 A:ASP277 4.9 32.4 1.0

Zinc binding site 2 out of 24 in 6oad

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Zinc binding site 2 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:27.4
occ:1.00
 OD2 A:ASP200 2.0 32.8 1.0
OD1 A:ASP277 2.1 32.4 1.0
OE2 A:GLU279 2.1 32.4 1.0
O A:ASP277 2.1 31.7 1.0
O A:HOH790 2.2 24.0 1.0
CG A:ASP200 3.0 29.0 1.0
CD A:GLU279 3.0 29.1 1.0
ZN A:ZN501 3.0 27.6 1.0
C A:ASP277 3.1 28.3 1.0
CG A:ASP277 3.2 29.3 1.0
OE1 A:GLU279 3.3 31.7 1.0
OD1 A:ASP200 3.3 28.9 1.0
O A:HOH670 3.3 41.7 1.0
CA A:ASP277 3.5 28.1 1.0
CB A:ASP277 3.9 29.0 1.0
NZ A:LYS207 4.0 31.3 1.0
O3 A:BCT505 4.0 28.3 1.0
OD2 A:ASP277 4.1 29.0 1.0
CE A:LYS207 4.3 30.8 1.0
N A:ALA278 4.3 28.0 1.0
N A:GLU279 4.3 26.1 1.0
CB A:ASP200 4.3 28.4 1.0
OD2 A:ASP218 4.3 32.0 1.0
CG A:GLU279 4.4 27.8 1.0
ND2 A:ASN250 4.5 24.8 1.0
C3 A:PGE509 4.6 71.8 1.0
NZ A:LYS195 4.7 32.0 1.0
CA A:ALA278 4.8 27.6 1.0
N A:ASP277 4.9 27.0 1.0
CB A:GLU279 4.9 26.8 1.0
CA A:GLY202 4.9 25.9 1.0
O A:THR276 4.9 25.8 1.0

Zinc binding site 3 out of 24 in 6oad

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Zinc binding site 3 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:28.4
occ:1.00
 OE1 B:GLU279 2.1 30.6 1.0
OD2 B:ASP218 2.1 35.1 1.0
NZ B:LYS195 2.1 33.2 1.0
O B:HOH741 2.2 31.7 1.0
OD2 B:ASP200 2.6 32.4 1.0
CG B:ASP218 2.7 31.2 1.0
OD1 B:ASP218 2.8 31.1 1.0
CE B:LYS195 2.9 31.0 1.0
CD B:GLU279 3.1 30.2 1.0
ZN B:ZN502 3.1 28.1 1.0
CG B:ASP200 3.4 28.4 1.0
OE2 B:GLU279 3.4 32.4 1.0
O2 B:BCT505 3.7 34.2 1.0
CB B:ASP200 3.9 27.7 1.0
O B:HOH787 4.0 35.0 1.0
CB B:ASP218 4.2 30.5 1.0
OD1 B:ASP200 4.2 28.3 1.0
O B:THR304 4.3 28.8 1.0
CD B:LYS195 4.3 30.7 1.0
CG B:GLU279 4.4 29.7 1.0
CG1 B:ILE197 4.5 26.2 1.0
CB B:ILE197 4.5 26.2 1.0
N B:GLY280 4.5 29.5 1.0
CG2 B:ILE197 4.6 26.0 1.0
O B:ASP277 4.7 30.9 1.0
CA B:GLY280 4.8 29.8 1.0
C B:BCT505 4.9 31.0 1.0

Zinc binding site 4 out of 24 in 6oad

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Zinc binding site 4 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:28.1
occ:1.00
 OE2 B:GLU279 2.0 32.4 1.0
OD2 B:ASP200 2.1 32.4 1.0
OD1 B:ASP277 2.1 30.8 1.0
O B:ASP277 2.1 30.9 1.0
O B:HOH741 2.2 31.7 1.0
CG B:ASP200 2.9 28.4 1.0
CD B:GLU279 3.0 30.2 1.0
OD1 B:ASP200 3.0 28.3 1.0
C B:ASP277 3.0 27.8 1.0
CG B:ASP277 3.1 28.1 1.0
ZN B:ZN501 3.1 28.4 1.0
OE1 B:GLU279 3.2 30.6 1.0
CA B:ASP277 3.4 27.3 1.0
O B:HOH787 3.7 35.0 1.0
CB B:ASP277 3.8 27.8 1.0
NZ B:LYS207 4.0 29.6 1.0
OD2 B:ASP277 4.1 28.3 1.0
O2 B:BCT505 4.2 34.2 1.0
CE B:LYS207 4.2 29.8 1.0
N B:ALA278 4.2 27.4 1.0
N B:GLU279 4.3 28.8 1.0
CB B:ASP200 4.3 27.7 1.0
CG B:GLU279 4.3 29.7 1.0
ND2 B:ASN250 4.4 24.2 1.0
OD2 B:ASP218 4.7 35.1 1.0
CA B:ALA278 4.7 28.2 1.0
N B:ASP277 4.8 26.3 1.0
CA B:GLY202 4.8 25.2 1.0
O B:THR276 4.8 25.2 1.0
NZ B:LYS195 4.8 33.2 1.0
CB B:GLU279 4.9 29.5 1.0

Zinc binding site 5 out of 24 in 6oad

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Zinc binding site 5 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:31.1
occ:1.00
 OD2 C:ASP218 2.0 35.1 1.0
OE1 C:GLU279 2.1 35.5 1.0
NZ C:LYS195 2.1 32.9 1.0
O C:HOH725 2.2 26.2 1.0
OD2 C:ASP200 2.6 30.6 1.0
CG C:ASP218 2.9 33.3 1.0
CE C:LYS195 2.9 31.7 1.0
ZN C:ZN502 3.0 29.5 1.0
OD1 C:ASP218 3.1 34.2 1.0
CD C:GLU279 3.1 33.1 1.0
OE2 C:GLU279 3.5 34.7 1.0
CG C:ASP200 3.5 28.3 1.0
O3 C:BCT505 3.6 29.6 1.0
O C:HOH753 3.9 40.2 1.0
CB C:ASP200 4.0 28.4 1.0
CB C:ASP218 4.3 32.0 1.0
CD C:LYS195 4.3 31.7 1.0
N C:GLY280 4.3 29.4 1.0
OD1 C:ASP200 4.4 27.5 1.0
O C:THR304 4.4 34.0 1.0
CG C:GLU279 4.4 32.2 1.0
O C:ASP277 4.5 31.9 1.0
CG1 C:ILE197 4.5 28.8 1.0
CA C:GLY280 4.6 29.9 1.0
CB C:ILE197 4.6 28.6 1.0
CG2 C:ILE197 4.6 28.4 1.0
C C:BCT505 4.9 29.6 1.0
OD1 C:ASP277 5.0 32.2 1.0

Zinc binding site 6 out of 24 in 6oad

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Zinc binding site 6 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn502

b:29.5
occ:1.00
 OD2 C:ASP200 2.1 30.6 1.0
OD1 C:ASP277 2.1 32.2 1.0
O C:ASP277 2.1 31.9 1.0
OE2 C:GLU279 2.1 34.7 1.0
O C:HOH725 2.2 26.2 1.0
CG C:ASP200 2.9 28.3 1.0
CD C:GLU279 3.0 33.1 1.0
ZN C:ZN501 3.0 31.1 1.0
C C:ASP277 3.1 29.6 1.0
OE1 C:GLU279 3.2 35.5 1.0
CG C:ASP277 3.2 30.4 1.0
OD1 C:ASP200 3.2 27.5 1.0
CA C:ASP277 3.5 29.4 1.0
O C:HOH753 3.6 40.2 1.0
CB C:ASP277 3.9 30.0 1.0
NZ C:LYS207 3.9 29.6 1.0
OD2 C:ASP277 4.1 31.0 1.0
CE C:LYS207 4.2 29.2 1.0
O3 C:BCT505 4.2 29.6 1.0
N C:ALA278 4.3 28.5 1.0
N C:GLU279 4.3 29.6 1.0
CB C:ASP200 4.3 28.4 1.0
OD2 C:ASP218 4.4 35.1 1.0
CG C:GLU279 4.4 32.2 1.0
ND2 C:ASN250 4.5 27.4 1.0
O C:HOH814 4.5 51.4 1.0
CA C:ALA278 4.7 29.1 1.0
CA C:GLY202 4.8 26.0 1.0
NZ C:LYS195 4.8 32.9 1.0
O C:THR276 4.8 29.6 1.0
N C:ASP277 4.9 29.1 1.0

Zinc binding site 7 out of 24 in 6oad

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Zinc binding site 7 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:28.3
occ:1.00
 OD2 D:ASP218 2.0 34.2 1.0
OE1 D:GLU279 2.1 30.9 1.0
NZ D:LYS195 2.1 32.8 1.0
O D:HOH747 2.2 28.9 1.0
OD2 D:ASP200 2.6 30.6 1.0
CG D:ASP218 2.7 31.3 1.0
OD1 D:ASP218 2.8 31.7 1.0
CE D:LYS195 2.9 30.6 1.0
ZN D:ZN502 3.1 28.6 1.0
CD D:GLU279 3.1 30.6 1.0
CG D:ASP200 3.5 27.7 1.0
OE2 D:GLU279 3.6 32.9 1.0
O1 D:BCT504 3.8 27.2 1.0
CB D:ASP200 4.0 27.1 1.0
O2 D:EDO508 4.1 47.2 1.0
CB D:ASP218 4.2 30.3 1.0
C2 D:EDO508 4.2 52.6 1.0
O D:THR304 4.2 31.5 1.0
CD D:LYS195 4.3 30.5 1.0
CG D:GLU279 4.4 29.9 1.0
OD1 D:ASP200 4.5 27.8 1.0
N D:GLY280 4.5 28.6 1.0
CG1 D:ILE197 4.6 26.3 1.0
CB D:ILE197 4.6 26.1 1.0
O D:ASP277 4.6 33.2 1.0
CG2 D:ILE197 4.6 25.8 1.0
CA D:GLY280 4.7 29.3 1.0
C D:BCT504 4.9 32.0 1.0
O D:ASP218 5.0 29.2 1.0
C1 D:EDO508 5.0 51.1 1.0

Zinc binding site 8 out of 24 in 6oad

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Zinc binding site 8 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:28.6
occ:1.00
 OD2 D:ASP200 2.1 30.6 1.0
OE2 D:GLU279 2.1 32.9 1.0
O D:ASP277 2.1 33.2 1.0
OD1 D:ASP277 2.1 32.3 1.0
O D:HOH747 2.2 28.9 1.0
CD D:GLU279 2.9 30.6 1.0
CG D:ASP200 2.9 27.7 1.0
C D:ASP277 3.0 29.8 1.0
OE1 D:GLU279 3.1 30.9 1.0
ZN D:ZN501 3.1 28.3 1.0
CG D:ASP277 3.2 31.0 1.0
OD1 D:ASP200 3.2 27.8 1.0
CA D:ASP277 3.4 29.8 1.0
O2 D:EDO508 3.7 47.2 1.0
CB D:ASP277 3.9 30.4 1.0
NZ D:LYS207 4.1 29.9 1.0
OD2 D:ASP277 4.1 32.2 1.0
CE D:LYS207 4.1 29.8 1.0
N D:ALA278 4.2 29.2 1.0
N D:GLU279 4.3 28.6 1.0
O1 D:BCT504 4.3 27.2 1.0
CG D:GLU279 4.3 29.9 1.0
CB D:ASP200 4.3 27.1 1.0
ND2 D:ASN250 4.4 25.4 1.0
OD2 D:ASP218 4.5 34.2 1.0
C4 D:PEG511 4.7 64.4 1.0
CA D:ALA278 4.7 29.1 1.0
CA D:GLY202 4.8 25.5 1.0
C2 D:EDO508 4.8 52.6 1.0
N D:ASP277 4.8 28.9 1.0
NZ D:LYS195 4.8 32.8 1.0
O D:THR276 4.9 27.4 1.0
CB D:GLU279 4.9 29.3 1.0

Zinc binding site 9 out of 24 in 6oad

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Zinc binding site 9 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:32.5
occ:1.00
 OD2 E:ASP218 2.1 36.4 1.0
OE1 E:GLU279 2.1 34.6 1.0
NZ E:LYS195 2.1 35.6 1.0
O E:HOH745 2.2 32.8 1.0
OD2 E:ASP200 2.7 29.9 1.0
CE E:LYS195 2.9 32.8 1.0
CG E:ASP218 2.9 34.2 1.0
ZN E:ZN502 3.0 30.3 1.0
CD E:GLU279 3.1 32.4 1.0
OD1 E:ASP218 3.2 32.6 1.0
OE2 E:GLU279 3.4 33.1 1.0
O1 E:BCT505 3.6 30.3 1.0
CG E:ASP200 3.6 28.4 1.0
O E:HOH725 3.9 39.2 1.0
CB E:ASP200 4.1 28.5 1.0
CB E:ASP218 4.3 33.0 1.0
CD E:LYS195 4.3 32.5 1.0
O E:THR304 4.4 32.6 1.0
N E:GLY280 4.4 30.2 1.0
CG E:GLU279 4.4 32.0 1.0
CG1 E:ILE197 4.5 28.9 1.0
O E:ASP277 4.5 34.0 1.0
OD1 E:ASP200 4.6 27.4 1.0
CB E:ILE197 4.7 28.4 1.0
CG2 E:ILE197 4.7 27.7 1.0
CA E:GLY280 4.7 30.2 1.0
C E:BCT505 4.9 30.4 1.0
OD1 E:ASP277 4.9 34.3 1.0

Zinc binding site 10 out of 24 in 6oad

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Zinc binding site 10 out of 24 in the 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:30.3
occ:1.00
 OE2 E:GLU279 2.1 33.1 1.0
OD2 E:ASP200 2.1 29.9 1.0
OD1 E:ASP277 2.1 34.3 1.0
O E:ASP277 2.1 34.0 1.0
O E:HOH745 2.2 32.8 1.0
CG E:ASP200 3.0 28.4 1.0
ZN E:ZN501 3.0 32.5 1.0
CD E:GLU279 3.0 32.4 1.0
C E:ASP277 3.0 31.7 1.0
CG E:ASP277 3.2 30.9 1.0
OE1 E:GLU279 3.3 34.6 1.0
OD1 E:ASP200 3.3 27.4 1.0
CA E:ASP277 3.4 30.8 1.0
O E:HOH725 3.6 39.2 1.0
CB E:ASP277 3.8 30.8 1.0
O1 E:BCT505 4.0 30.3 1.0
OD2 E:ASP277 4.1 28.7 1.0
NZ E:LYS207 4.1 35.2 1.0
N E:ALA278 4.2 31.2 1.0
CE E:LYS207 4.3 35.0 1.0
N E:GLU279 4.3 30.4 1.0
OD2 E:ASP218 4.3 36.4 1.0
CB E:ASP200 4.3 28.5 1.0
CG E:GLU279 4.4 32.0 1.0
ND2 E:ASN250 4.5 27.3 1.0
C3 E:PEG509 4.5 61.4 1.0
CA E:ALA278 4.7 31.0 1.0
NZ E:LYS195 4.8 35.6 1.0
N E:ASP277 4.8 30.0 1.0
C4 E:PEG509 4.8 59.8 1.0
CA E:GLY202 4.8 26.5 1.0
O E:THR276 4.9 30.2 1.0
CB E:GLU279 4.9 31.3 1.0

Reference:

G.Minasov, L.Shuvalova, Z.Wawrzak, O.Kiryukhina, S.Grimshaw, K.Kwon, K.J.F.Satchell, Center For Structural Genomics Of Infectious Diseases(Csgid). 2.05 Angstrom Resolution Crystal Structure of Aminopeptidase B From Escherichia Coli Str. K-12 Substr. MG1655. To Be Published.
Page generated: Tue Oct 29 04:12:32 2024

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