Zinc in PDB 6f06: Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

Enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide

All present enzymatic activity of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide:
3.4.22.15;

Protein crystallography data

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06 was solved by A.Kuglstatter, M.Stihle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.48 / 2.02
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 43.040, 50.791, 84.911, 90.00, 91.53, 90.00
R / Rfree (%) 20.1 / 27.4

Other elements in 6f06:

The structure of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide (pdb code 6f06). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide, PDB code: 6f06:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 6f06

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Zinc binding site 1 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:29.5
occ:1.00
ND1 A:HIS163 1.9 24.0 1.0
O A:HOH402 2.1 23.6 1.0
SG A:CYS25 2.3 32.2 1.0
CL A:CL308 2.3 37.1 1.0
CE1 A:HIS163 2.8 24.4 1.0
CB A:CYS25 2.9 27.7 1.0
CG A:HIS163 3.0 23.9 1.0
N30 A:C7T301 3.2 36.6 1.0
CB A:HIS163 3.5 25.0 1.0
C29 A:C7T301 3.5 35.6 1.0
CA A:HIS163 3.6 27.1 1.0
O A:ASP162 4.0 30.3 1.0
NE2 A:HIS163 4.0 24.1 1.0
CD2 A:HIS163 4.1 22.1 1.0
CA A:CYS25 4.2 27.2 1.0
N A:GLY164 4.3 25.6 1.0
C2 A:C7T301 4.3 36.0 1.0
C A:HIS163 4.4 26.2 1.0
N16 A:C7T301 4.4 35.1 1.0
N A:CYS25 4.5 27.9 1.0
OE1 A:GLN19 4.6 26.3 1.0
N A:HIS163 4.7 27.2 1.0
NE2 A:GLN19 4.7 28.2 1.0
C A:ASP162 4.7 29.0 1.0

Zinc binding site 2 out of 14 in 6f06

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Zinc binding site 2 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn303

b:38.2
occ:1.00
OD2 A:ASP137 1.9 33.0 1.0
NE2 A:HIS140 2.1 35.8 1.0
CG A:ASP137 2.7 31.6 1.0
OD1 A:ASP137 2.9 32.1 1.0
CE1 A:HIS140 2.9 36.7 1.0
CD2 A:HIS140 3.2 34.1 1.0
O A:ASP155 3.8 44.7 1.0
N A:SER157 3.8 36.9 1.0
ND1 A:HIS140 4.0 36.7 1.0
CB A:ASP137 4.2 29.8 1.0
CG A:HIS140 4.2 36.6 1.0
CA A:CYS156 4.2 38.0 1.0
CB A:SER157 4.3 43.6 1.0
C A:CYS156 4.4 37.3 1.0
CB A:ASP160 4.5 53.1 1.0
C A:ASP155 4.7 41.6 1.0
CA A:SER157 4.7 40.9 1.0
O A:ASP160 4.8 37.4 1.0
O A:GLY139 4.8 43.7 1.0
N A:CYS156 4.9 39.4 1.0
SG A:CYS156 5.0 31.9 1.0

Zinc binding site 3 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 3 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn304

b:28.3
occ:1.00
OE2 A:GLU86 1.9 26.2 1.0
OE1 A:GLU50 1.9 18.1 1.0
O A:HOH434 1.9 34.7 1.0
O A:HOH447 2.1 10.8 1.0
CD A:GLU50 2.9 18.2 1.0
CD A:GLU86 2.9 27.3 1.0
OE2 A:GLU50 3.2 19.7 1.0
O A:LEU48 3.4 23.2 1.0
CG A:GLU86 3.7 27.3 1.0
OE1 A:GLU86 3.8 26.8 1.0
CB A:GLU86 4.0 25.3 1.0
O A:HOH417 4.0 21.2 1.0
O A:HOH409 4.1 32.2 1.0
CE2 A:PHE28 4.1 22.0 1.0
CG A:GLU50 4.2 18.6 1.0
CB A:TYR91 4.2 24.8 1.0
N A:GLU50 4.3 18.5 1.0
CD A:LYS17 4.5 35.0 1.0
C A:LEU48 4.5 23.1 1.0
CB A:GLU50 4.5 18.4 1.0
CZ A:PHE28 4.6 22.8 1.0
CA A:SER49 4.8 21.2 1.0
CG A:LYS17 4.8 29.3 1.0
CA A:GLU86 4.9 25.4 1.0
CD2 A:PHE28 5.0 22.3 1.0
CG A:TYR91 5.0 27.3 1.0

Zinc binding site 4 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 4 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn305

b:42.6
occ:1.00
O A:HOH403 1.8 23.9 1.0
OE1 A:GLU96 2.1 37.5 1.0
OE1 A:GLU92 2.2 35.0 1.0
OE2 A:GLU96 2.2 35.6 1.0
CD A:GLU96 2.5 36.7 1.0
OE2 A:GLU92 2.6 31.7 1.0
CD A:GLU92 2.7 32.5 1.0
CG A:GLU96 4.0 34.9 1.0
CG A:GLU92 4.2 31.1 1.0
NZ A:LYS99 4.7 38.1 1.0
CB A:GLU96 4.8 33.6 1.0
CB A:GLU92 4.9 30.7 1.0
O A:HOH452 5.0 30.1 1.0

Zinc binding site 5 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 5 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn306

b:31.5
occ:1.00
OD2 A:ASP71 1.8 25.8 1.0
OD1 A:ASP114 1.9 28.1 1.0
CG A:ASP71 2.8 23.4 1.0
CG A:ASP114 2.9 28.3 1.0
OD1 A:ASP71 3.1 23.3 1.0
OD2 A:ASP114 3.2 28.8 1.0
O A:HOH446 3.8 33.8 1.0
CB A:SER216 4.1 27.8 1.0
CB A:ASP71 4.1 23.1 1.0
CB A:ASP114 4.1 27.8 1.0
CE2 A:PHE112 4.2 27.8 1.0
OG A:SER216 4.4 26.6 1.0
O A:HOH444 4.5 23.0 1.0
CA A:ASP114 4.6 27.1 1.0
CD2 A:PHE112 4.7 28.4 1.0

Zinc binding site 6 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 6 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn307

b:67.9
occ:1.00
ND1 A:HIS140 2.1 36.7 1.0
OD2 A:ASP155 2.6 49.2 1.0
OE2 A:GLU153 2.7 38.5 1.0
CD A:GLU153 2.8 37.5 1.0
CG A:HIS140 2.8 36.6 1.0
CE1 A:HIS140 3.0 36.7 1.0
CB A:HIS140 3.2 35.3 1.0
OE1 A:GLU153 3.2 40.0 1.0
CG A:GLU153 3.4 35.1 1.0
CG A:ASP155 3.5 52.8 1.0
O A:HOH443 3.8 30.2 1.0
OD1 A:ASP155 3.8 61.4 1.0
CD2 A:HIS140 3.9 34.1 1.0
NE2 A:HIS140 3.9 35.8 1.0
CA A:HIS140 4.3 35.9 1.0
CB A:ASP155 4.7 48.5 1.0
N A:ASP155 4.8 40.8 1.0
C A:ASP155 4.8 41.6 1.0
CB A:GLU153 4.9 33.0 1.0
OG A:SER142 4.9 31.7 1.0
CA A:ASP155 4.9 43.5 1.0

Zinc binding site 7 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 7 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:28.9
occ:1.00
O B:HOH408 2.0 35.0 1.0
ND1 B:HIS163 2.1 26.2 1.0
CL B:CL310 2.2 33.4 1.0
SG B:CYS25 2.3 25.7 1.0
CE1 B:HIS163 3.0 23.9 1.0
CB B:CYS25 3.0 24.7 1.0
N30 B:C7T301 3.1 32.8 1.0
CG B:HIS163 3.1 26.1 1.0
CB B:HIS163 3.5 25.7 1.0
CA B:HIS163 3.6 24.2 1.0
C29 B:C7T301 3.6 33.1 1.0
O B:ASP162 3.9 27.0 1.0
NE2 B:HIS163 4.1 25.2 1.0
CD2 B:HIS163 4.2 23.8 1.0
N B:GLY164 4.3 25.8 1.0
CA B:CYS25 4.3 24.3 1.0
C B:HIS163 4.4 24.6 1.0
N B:CYS25 4.5 24.7 1.0
C2 B:C7T301 4.6 34.3 1.0
N B:HIS163 4.6 24.7 1.0
NE2 B:GLN19 4.6 21.9 1.0
C B:ASP162 4.7 28.0 1.0
N16 B:C7T301 4.7 35.4 1.0
OE1 B:GLN19 4.9 22.6 1.0
CZ2 B:TRP189 4.9 27.5 1.0
NE1 B:TRP189 5.0 27.2 1.0

Zinc binding site 8 out of 14 in 6f06

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Zinc binding site 8 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn303

b:42.6
occ:1.00
OD2 B:ASP137 1.9 32.5 1.0
O B:HOH441 2.0 43.7 1.0
NE2 B:HIS140 2.1 35.4 1.0
CG B:ASP137 2.8 33.4 1.0
CE1 B:HIS140 2.8 35.2 1.0
OD1 B:ASP137 3.0 31.4 1.0
CD2 B:HIS140 3.2 33.7 1.0
ND1 B:HIS140 4.0 33.1 1.0
O B:ASP155 4.0 34.7 1.0
N B:SER157 4.1 30.5 1.0
CB B:ASP137 4.2 31.3 1.0
CG B:HIS140 4.2 34.2 1.0
CA B:CYS156 4.3 32.2 1.0
CB B:SER157 4.3 36.7 1.0
C B:CYS156 4.5 31.2 1.0
CA B:SER157 4.8 35.7 1.0
C B:ASP155 4.9 33.1 1.0
O B:ASP160 5.0 40.7 1.0
SG B:CYS156 5.0 31.3 1.0

Zinc binding site 9 out of 14 in 6f06

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Zinc binding site 9 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn304

b:35.7
occ:1.00
OE1 B:GLU9 1.9 30.1 1.0
OD2 B:ASP6 2.2 33.4 1.0
CD B:GLU9 3.0 33.1 1.0
CG B:ASP6 3.1 32.4 1.0
CB B:ASP6 3.3 33.2 1.0
CG B:GLU9 3.5 32.2 1.0
NH2 B:ARG8 3.8 27.6 1.0
OE2 B:GLU9 4.1 32.7 1.0
OD1 B:ASP6 4.2 34.0 1.0
CZ B:ARG8 4.7 27.1 1.0
NE B:ARG8 4.7 26.8 1.0
CA B:ASP6 4.9 31.1 1.0
CB B:GLU9 4.9 31.1 1.0

Zinc binding site 10 out of 14 in 6f06

Go back to Zinc Binding Sites List in 6f06
Zinc binding site 10 out of 14 in the Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Cathepsin L in Complex with (3S,14E)-8-(Azetidin-3-Yl)-19-Chloro-N-(1- Cyanocyclopropyl)-5-Oxo-12,17-Dioxa-4-Azatricyclo[16.2.2.06, 11]Docosa-1(21),6,8,10,14,18(22),19-Heptaene-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn305

b:33.6
occ:1.00
OE2 B:GLU86 1.9 32.1 1.0
OE1 B:GLU50 2.0 32.7 1.0
O B:HOH419 2.0 26.9 1.0
O B:HOH434 2.1 21.5 1.0
CD B:GLU50 2.8 29.4 1.0
CD B:GLU86 2.9 34.4 1.0
OE2 B:GLU50 2.9 29.7 1.0
O B:LEU48 3.4 30.4 1.0
CG B:GLU86 3.5 32.5 1.0
OE1 B:GLU86 3.8 37.5 1.0
O B:HOH414 3.9 31.6 1.0
O B:HOH421 3.9 32.5 1.0
CB B:GLU86 4.0 34.4 1.0
CG B:GLU50 4.2 29.0 1.0
N B:GLU50 4.2 33.3 1.0
OG B:SER47 4.3 41.3 1.0
CE2 B:PHE28 4.4 22.2 1.0
CE B:LYS17 4.4 25.9 1.0
CB B:TYR91 4.4 32.4 1.0
C B:LEU48 4.5 32.2 1.0
CB B:GLU50 4.6 28.0 1.0
CG B:LYS17 4.7 24.3 1.0
CZ B:PHE28 4.9 21.9 1.0
CA B:SER49 4.9 34.6 1.0
CA B:GLU86 4.9 36.3 1.0
CD B:LYS17 5.0 25.0 1.0

Reference:

M.Giroud, U.Dietzel, L.Anselm, D.Banner, A.Kuglstatter, J.Benz, J.B.Blanc, D.Gaufreteau, H.Liu, X.Lin, A.Stich, B.Kuhn, F.Schuler, M.Kaiser, R.Brun, T.Schirmeister, C.Kisker, F.Diederich, W.Haap. Repurposing A Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams As Potent Rhodesain and Trypanosoma Brucei Inhibitors. J. Med. Chem. V. 61 3350 2018.
ISSN: ISSN 1520-4804
PubMed: 29590750
DOI: 10.1021/ACS.JMEDCHEM.7B01869
Page generated: Wed Dec 16 11:45:24 2020

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