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Zinc in PDB 3v9b: Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide

Enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide

All present enzymatic activity of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide, PDB code: 3v9b was solved by H.T.Kim, H.J.Chang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.41 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 98.587, 110.293, 161.607, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 23.6

Other elements in 3v9b:

The structure of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide also contains other interesting chemical elements:

Fluorine (F) 8 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide (pdb code 3v9b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide, PDB code: 3v9b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 1 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:23.4
occ:1.00
 OD2 A:ASP201 2.1 15.8 1.0
OD1 A:ASP318 2.2 19.1 1.0
O A:HOH24 2.3 15.6 1.0
O A:HOH499 2.3 19.6 1.0
NE2 A:HIS164 2.3 16.7 1.0
NE2 A:HIS200 2.3 21.9 1.0
CD2 A:HIS200 3.0 17.1 1.0
CG A:ASP318 3.1 18.5 1.0
CD2 A:HIS164 3.2 15.8 1.0
CG A:ASP201 3.2 15.9 1.0
CE1 A:HIS164 3.3 15.8 1.0
OD2 A:ASP318 3.4 20.6 1.0
CE1 A:HIS200 3.4 17.8 1.0
ZN A:ZN502 3.8 42.0 1.0
OD1 A:ASP201 3.8 16.2 1.0
O A:HOH500 4.0 14.5 1.0
O A:HOH21 4.0 15.2 1.0
CD2 A:HIS160 4.2 18.5 1.0
CG A:HIS200 4.3 18.4 1.0
CG A:HIS164 4.4 18.2 1.0
CB A:ASP201 4.4 14.6 1.0
ND1 A:HIS164 4.4 17.3 1.0
ND1 A:HIS200 4.4 17.2 1.0
NE2 A:HIS160 4.4 17.6 1.0
CB A:ASP318 4.5 16.2 1.0
CG2 A:VAL168 4.7 13.5 1.0
O A:HOH30 4.8 14.5 1.0
C35 A:IHM1 4.9 23.8 1.0

Zinc binding site 2 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 2 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:42.0
occ:1.00
 O A:HOH30 2.3 14.5 1.0
O A:HOH24 2.3 15.6 1.0
OD1 A:ASP201 2.3 16.2 1.0
O A:HOH500 2.3 14.5 1.0
O A:HOH2 2.3 12.9 1.0
O A:HOH503 2.4 12.8 1.0
CG A:ASP201 3.2 15.9 1.0
OD2 A:ASP201 3.4 15.8 1.0
ZN A:ZN501 3.8 23.4 1.0
O A:HOH499 3.9 19.6 1.0
O A:HIS200 4.0 12.8 1.0
OE2 A:GLU230 4.1 17.1 1.0
CD2 A:HIS200 4.2 17.1 1.0
NE2 A:HIS233 4.2 11.6 1.0
O17 A:IHM1 4.2 38.0 1.0
OG1 A:THR271 4.3 17.4 1.0
O A:HOH460 4.3 19.5 1.0
N37 A:IHM1 4.3 28.7 1.0
C36 A:IHM1 4.3 28.5 1.0
CD2 A:HIS233 4.4 13.4 1.0
CB A:ASP201 4.6 14.6 1.0
OD2 A:ASP318 4.6 20.6 1.0
CD2 A:HIS204 4.7 15.9 1.0
NE2 A:HIS200 4.7 21.9 1.0
CB A:THR271 4.8 19.1 1.0
CD2 A:HIS160 4.8 18.5 1.0
NE2 A:HIS160 4.8 17.6 1.0
O A:THR271 4.8 18.6 1.0
CA A:ASP201 4.9 14.4 1.0
NE2 A:HIS204 4.9 16.6 1.0
CD A:GLU230 4.9 17.3 1.0
C A:HIS200 4.9 12.9 1.0
C38 A:IHM1 5.0 27.0 1.0
CG A:GLU230 5.0 13.7 1.0
C35 A:IHM1 5.0 23.8 1.0

Zinc binding site 3 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 3 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:23.9
occ:1.00
 OD1 B:ASP318 2.2 14.9 1.0
OD2 B:ASP201 2.3 21.7 1.0
O B:HOH23 2.3 16.9 1.0
NE2 B:HIS200 2.3 14.0 1.0
O B:HOH493 2.3 20.4 1.0
NE2 B:HIS164 2.3 23.5 1.0
CD2 B:HIS200 3.0 11.3 1.0
CG B:ASP318 3.2 21.1 1.0
CG B:ASP201 3.2 19.2 1.0
CD2 B:HIS164 3.3 23.0 1.0
CE1 B:HIS164 3.3 23.2 1.0
CE1 B:HIS200 3.4 12.9 1.0
OD2 B:ASP318 3.5 21.9 1.0
OD1 B:ASP201 3.7 20.3 1.0
ZN B:ZN504 3.8 46.8 1.0
O B:HOH7 4.0 15.3 1.0
O B:HOH494 4.1 14.4 1.0
CD2 B:HIS160 4.2 16.7 1.0
CG B:HIS200 4.2 13.5 1.0
ND1 B:HIS200 4.4 11.0 1.0
CB B:ASP201 4.4 18.0 1.0
ND1 B:HIS164 4.4 23.4 1.0
CG B:HIS164 4.4 22.8 1.0
NE2 B:HIS160 4.5 16.3 1.0
CB B:ASP318 4.5 19.0 1.0
CG2 B:VAL168 4.6 14.4 1.0
O B:HOH67 4.9 16.8 1.0
C35 B:IHM1 5.0 22.7 1.0
CA B:ASP318 5.0 19.7 1.0

Zinc binding site 4 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 4 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:46.8
occ:1.00
 OD1 B:ASP201 2.2 20.3 1.0
O B:HOH67 2.3 16.8 1.0
O B:HOH23 2.4 16.9 1.0
O B:HOH22 2.4 15.8 1.0
O B:HOH494 2.4 14.4 1.0
O B:HOH4 2.5 13.9 1.0
CG B:ASP201 3.1 19.2 1.0
OD2 B:ASP201 3.4 21.7 1.0
ZN B:ZN503 3.8 23.9 1.0
O B:HIS200 4.0 16.3 1.0
O B:HOH493 4.1 20.4 1.0
OE2 B:GLU230 4.2 18.2 1.0
C36 B:IHM1 4.2 27.6 1.0
OG1 B:THR271 4.2 19.8 1.0
NE2 B:HIS233 4.2 15.3 1.0
CD2 B:HIS200 4.3 11.3 1.0
O17 B:IHM1 4.4 33.5 1.0
N37 B:IHM1 4.4 27.2 1.0
O B:HOH62 4.4 17.5 1.0
CD2 B:HIS233 4.4 18.4 1.0
CB B:ASP201 4.5 18.0 1.0
CD2 B:HIS204 4.6 16.0 1.0
O B:THR271 4.6 20.0 1.0
OD2 B:ASP318 4.7 21.9 1.0
CB B:THR271 4.7 22.1 1.0
NE2 B:HIS200 4.7 14.0 1.0
NE2 B:HIS160 4.7 16.3 1.0
CD2 B:HIS160 4.8 16.7 1.0
NE2 B:HIS204 4.8 16.7 1.0
CA B:ASP201 4.8 14.9 1.0
C35 B:IHM1 4.9 22.7 1.0
C B:HIS200 4.9 14.7 1.0
CD B:GLU230 5.0 19.2 1.0

Zinc binding site 5 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 5 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn505

b:25.1
occ:1.00
 OD2 C:ASP201 2.2 17.1 1.0
NE2 C:HIS164 2.3 18.2 1.0
OD1 C:ASP318 2.3 24.8 1.0
O C:HOH501 2.3 22.2 1.0
NE2 C:HIS200 2.4 14.2 1.0
O C:HOH29 2.4 20.9 1.0
CD2 C:HIS200 3.0 13.2 1.0
CG C:ASP318 3.2 25.2 1.0
CG C:ASP201 3.2 14.6 1.0
CD2 C:HIS164 3.2 20.9 1.0
CE1 C:HIS164 3.3 20.5 1.0
OD2 C:ASP318 3.5 22.8 1.0
CE1 C:HIS200 3.5 14.8 1.0
ZN C:ZN506 3.7 46.7 1.0
OD1 C:ASP201 3.8 16.6 1.0
CD2 C:HIS160 4.1 17.9 1.0
O C:HOH500 4.2 16.8 1.0
O C:HOH17 4.2 17.2 1.0
CG C:HIS200 4.3 16.4 1.0
CB C:ASP201 4.4 16.6 1.0
ND1 C:HIS164 4.4 19.6 1.0
CG C:HIS164 4.4 21.4 1.0
ND1 C:HIS200 4.5 13.6 1.0
NE2 C:HIS160 4.5 15.8 1.0
CB C:ASP318 4.6 20.1 1.0
CG2 C:VAL168 4.8 18.1 1.0
O C:HOH36 4.8 18.9 1.0
C35 C:IHM1 5.0 26.5 1.0

Zinc binding site 6 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 6 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn506

b:46.7
occ:1.00
 OD1 C:ASP201 2.3 16.6 1.0
O C:HOH36 2.3 18.9 1.0
O C:HOH29 2.3 20.9 1.0
O C:HOH19 2.4 12.7 1.0
O C:HOH502 2.4 18.1 1.0
O C:HOH500 2.5 16.8 1.0
CG C:ASP201 3.2 14.6 1.0
OD2 C:ASP201 3.3 17.1 1.0
ZN C:ZN505 3.7 25.1 1.0
O C:HIS200 4.1 18.0 1.0
OE2 C:GLU230 4.1 16.0 1.0
O C:HOH501 4.1 22.2 1.0
CD2 C:HIS200 4.2 13.2 1.0
OG1 C:THR271 4.2 19.3 1.0
NE2 C:HIS233 4.3 11.8 1.0
C36 C:IHM1 4.3 29.9 1.0
O17 C:IHM1 4.3 36.6 1.0
N37 C:IHM1 4.4 29.3 1.0
O C:HOH42 4.4 17.0 1.0
CD2 C:HIS233 4.4 12.2 1.0
CB C:ASP201 4.6 16.6 1.0
CD2 C:HIS204 4.6 14.9 1.0
CD2 C:HIS160 4.6 17.9 1.0
OD2 C:ASP318 4.7 22.8 1.0
O C:THR271 4.7 18.0 1.0
NE2 C:HIS160 4.7 15.8 1.0
NE2 C:HIS200 4.8 14.2 1.0
CB C:THR271 4.8 20.1 1.0
NE2 C:HIS204 4.8 15.7 1.0
CA C:ASP201 4.9 15.9 1.0
C C:HIS200 5.0 16.3 1.0
C35 C:IHM1 5.0 26.5 1.0

Zinc binding site 7 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 7 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn507

b:20.5
occ:1.00
 O D:HOH439 2.2 10.3 1.0
OD1 D:ASP318 2.2 14.8 1.0
OD2 D:ASP201 2.2 18.1 1.0
NE2 D:HIS164 2.3 14.6 1.0
O D:HOH505 2.3 19.7 1.0
NE2 D:HIS200 2.3 10.0 1.0
CD2 D:HIS200 3.1 9.7 1.0
CG D:ASP318 3.1 15.3 1.0
CG D:ASP201 3.2 17.3 1.0
CD2 D:HIS164 3.2 14.9 1.0
CE1 D:HIS164 3.2 14.9 1.0
OD2 D:ASP318 3.3 15.0 1.0
CE1 D:HIS200 3.4 11.9 1.0
OD1 D:ASP201 3.7 16.6 1.0
ZN D:ZN508 3.8 43.0 1.0
CD2 D:HIS160 4.1 15.4 1.0
O D:HOH510 4.1 19.1 1.0
O D:HOH10 4.1 15.5 1.0
NE2 D:HIS160 4.3 15.7 1.0
CG D:HIS200 4.3 11.6 1.0
CB D:ASP201 4.3 16.7 1.0
ND1 D:HIS164 4.3 13.6 1.0
CG D:HIS164 4.4 16.8 1.0
ND1 D:HIS200 4.4 10.6 1.0
CB D:ASP318 4.5 14.6 1.0
CG2 D:VAL168 4.7 15.5 1.0
O D:HOH506 5.0 13.2 1.0
CA D:ASP318 5.0 14.9 1.0

Zinc binding site 8 out of 8 in 3v9b

Go back to Zinc Binding Sites List in 3v9b
Zinc binding site 8 out of 8 in the Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of the Catalytic Domain of PDE4D2 with (S)-N-(3-{1- [1-(3-Cyclopropylmethoxy-4-Difluoromethoxyphenyl)-2-(1-Oxypyridin-4- Yl)-Ethyl]-1H-Pyrazl-3-Yl}Phenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn508

b:43.0
occ:1.00
 OD1 D:ASP201 2.2 16.6 1.0
O D:HOH439 2.3 10.3 1.0
O D:HOH509 2.3 10.2 1.0
O D:HOH506 2.3 13.2 1.0
O D:HOH14 2.4 12.6 1.0
O D:HOH510 2.4 19.1 1.0
CG D:ASP201 3.2 17.3 1.0
OD2 D:ASP201 3.5 18.1 1.0
ZN D:ZN507 3.8 20.5 1.0
OE2 D:GLU230 4.0 20.9 1.0
NE2 D:HIS233 4.1 15.5 1.0
O D:HIS200 4.1 13.3 1.0
O D:HOH505 4.2 19.7 1.0
OG1 D:THR271 4.3 12.8 1.0
C36 D:IHM1 4.3 21.6 1.0
CD2 D:HIS200 4.3 9.7 1.0
O17 D:IHM1 4.4 32.8 1.0
O D:HOH63 4.4 18.1 1.0
CD2 D:HIS233 4.4 14.3 1.0
N37 D:IHM1 4.4 24.7 1.0
CB D:ASP201 4.5 16.7 1.0
OD2 D:ASP318 4.6 15.0 1.0
CD2 D:HIS204 4.6 15.5 1.0
NE2 D:HIS160 4.7 15.7 1.0
NE2 D:HIS200 4.8 10.0 1.0
CD2 D:HIS160 4.8 15.4 1.0
CB D:THR271 4.8 15.4 1.0
O D:THR271 4.8 17.5 1.0
CA D:ASP201 4.8 15.4 1.0
CD D:GLU230 4.9 20.6 1.0
C35 D:IHM1 4.9 21.1 1.0
CG D:GLU230 5.0 18.9 1.0
NE2 D:HIS204 5.0 16.5 1.0
C D:HIS200 5.0 13.2 1.0

Reference:

C.M.Park, D.J.Jeon. Stereoselective Synthesis of Novel Pyrazole Derivatives Using Tert-Butansulfonamide As A Chiral Auxiliary Org.Biomol.Chem. V. 10 2613 2012.
ISSN: ISSN 1477-0520
PubMed: 22371117
DOI: 10.1039/C2OB06495B
Page generated: Sat Oct 26 17:38:54 2024

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