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Calcium in PDB 4omd: X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba

Enzymatic activity of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba

All present enzymatic activity of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba:
3.4.21.75;

Protein crystallography data

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba, PDB code: 4omd was solved by S.O.Dahms, M.E.Than, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 141.616, 152.612, 168.538, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 21.8

Other elements in 4omd:

The structure of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba also contains other interesting chemical elements:

Sodium (Na) 6 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba (pdb code 4omd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba, PDB code: 4omd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 4omd

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Calcium binding site 1 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca603

b:18.2
occ:1.00
 O A:VAL210 2.3 21.4 1.0
O A:VAL205 2.4 14.6 1.0
OD2 A:ASP115 2.4 17.9 1.0
OD1 A:ASP162 2.4 22.5 1.0
O A:GLY212 2.4 19.1 1.0
OD1 A:ASN208 2.4 23.0 1.0
OD2 A:ASP162 2.7 29.1 1.0
CG A:ASP162 2.8 24.2 1.0
CG A:ASP115 3.4 19.4 1.0
C A:VAL210 3.5 20.1 1.0
C A:VAL205 3.5 16.4 1.0
CG A:ASN208 3.5 20.3 1.0
C A:GLY212 3.6 20.3 1.0
ND2 A:ASN208 4.0 18.3 1.0
CB A:ASP115 4.1 20.5 1.0
N A:GLY212 4.2 22.9 1.0
CA A:VAL210 4.2 17.4 1.0
N A:VAL210 4.2 16.6 1.0
C A:CYS211 4.3 23.1 1.0
CB A:VAL210 4.3 17.1 1.0
OD1 A:ASP115 4.3 17.5 1.0
CB A:ASP162 4.3 22.2 1.0
CA A:GLY212 4.4 20.5 1.0
N A:ALA206 4.4 15.8 1.0
CA A:VAL205 4.4 15.8 1.0
CA A:ALA206 4.5 18.0 1.0
N A:VAL205 4.5 17.1 1.0
O A:CYS211 4.5 20.7 1.0
N A:CYS211 4.5 21.1 1.0
CG1 A:VAL213 4.6 21.9 1.0
N A:VAL213 4.6 19.8 1.0
CA A:VAL213 4.7 20.4 1.0
CB A:VAL205 4.7 18.2 1.0
N A:ASN208 4.8 19.6 1.0
CA A:CYS211 4.8 22.7 1.0
CB A:ASN208 4.8 17.8 1.0
C A:ALA204 4.8 19.0 1.0
CB A:CYS211 4.9 24.1 1.0
C A:ALA206 4.9 19.8 1.0
N A:ASN207 5.0 19.8 1.0
CG1 A:VAL210 5.0 15.4 1.0
CB A:ALA204 5.0 18.3 1.0

Calcium binding site 2 out of 18 in 4omd

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Calcium binding site 2 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca604

b:15.1
occ:1.00
 OD1 A:ASP258 2.2 22.2 1.0
O A:HOH746 2.2 29.6 1.0
OD2 A:ASP301 2.3 25.7 1.0
O A:HOH796 2.3 8.4 1.0
OE1 A:GLU331 2.4 17.4 1.0
OE2 A:GLU331 2.6 20.6 1.0
O A:HOH758 2.7 31.8 1.0
CD A:GLU331 2.8 17.1 1.0
CG A:ASP301 3.3 23.5 1.0
CG A:ASP258 3.4 22.6 1.0
OD1 A:ASP301 4.1 20.1 1.0
N34 H:00S5 4.1 18.4 1.0
CB A:ASP258 4.1 22.4 1.0
CB A:ASP301 4.2 24.6 1.0
OD2 A:ASP258 4.3 22.3 1.0
CA A:ASP258 4.3 22.0 1.0
O A:SER293 4.3 24.6 1.0
CG A:GLU331 4.4 18.7 1.0
OD2 A:ASP306 4.4 25.2 1.0
O A:SER302 4.5 28.7 1.0
CA A:GLY294 4.6 17.8 1.0
C27 H:00S5 4.7 19.3 1.0
CB A:ASP306 4.7 19.6 1.0
CA A:CYS303 4.8 25.1 1.0
O A:GLU257 4.8 26.5 1.0
N A:GLY296 4.8 15.2 1.0
C A:SER302 4.9 27.3 1.0
O A:PRO256 4.9 20.0 1.0

Calcium binding site 3 out of 18 in 4omd

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Calcium binding site 3 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca605

b:35.4
occ:1.00
 O A:HOH727 2.3 13.1 1.0
O A:HOH723 2.4 28.2 1.0
O A:ASP181 2.4 30.1 1.0
OD2 A:ASP174 2.4 22.4 1.0
O A:HOH809 2.5 24.4 1.0
OD1 A:ASP179 2.7 24.1 1.0
OD2 A:ASP179 2.7 29.1 1.0
CG A:ASP179 3.0 26.1 1.0
CG A:ASP174 3.4 21.5 1.0
C A:ASP181 3.5 28.9 1.0
CB A:ASP174 3.7 21.4 1.0
CB A:ASP181 3.9 31.8 1.0
CA A:ASP181 4.2 29.3 1.0
CG A:ASP181 4.5 34.7 1.0
N A:ASP181 4.5 28.9 1.0
CB A:ASP179 4.5 24.3 1.0
OD1 A:ASP174 4.6 19.7 1.0
NH2 A:ARG225 4.6 21.0 1.0
N A:PRO182 4.6 27.3 1.0
O A:GLN183 4.7 23.1 1.0
OD1 A:ASP181 4.8 37.3 1.0
CB A:ASP177 4.8 31.6 1.0
N A:GLN183 4.8 24.7 1.0
OD2 A:ASP177 4.9 35.8 1.0
CA A:PRO182 5.0 25.7 1.0

Calcium binding site 4 out of 18 in 4omd

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Calcium binding site 4 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:32.4
occ:1.00
 OD2 B:ASP115 2.2 30.9 1.0
O B:GLY212 2.2 27.3 1.0
O B:VAL205 2.3 20.1 1.0
O B:VAL210 2.3 27.7 1.0
OD1 B:ASP162 2.4 40.0 1.0
OD1 B:ASN208 2.6 33.5 1.0
OD2 B:ASP162 2.7 39.6 1.0
CG B:ASP162 2.9 38.3 1.0
CG B:ASP115 3.3 29.9 1.0
C B:GLY212 3.5 26.1 1.0
C B:VAL205 3.5 23.9 1.0
C B:VAL210 3.5 29.4 1.0
CG B:ASN208 3.6 31.9 1.0
ND2 B:ASN208 4.0 31.7 1.0
N B:GLY212 4.1 29.2 1.0
CB B:ASP115 4.1 29.9 1.0
OD1 B:ASP115 4.2 30.0 1.0
C B:CYS211 4.2 30.5 1.0
CA B:GLY212 4.3 26.2 1.0
CA B:VAL210 4.3 28.6 1.0
N B:VAL210 4.3 27.8 1.0
N B:ALA206 4.4 24.0 1.0
CA B:ALA206 4.4 26.1 1.0
CA B:VAL205 4.4 24.3 1.0
CB B:VAL210 4.4 27.8 1.0
CB B:ASP162 4.4 35.6 1.0
CG1 B:VAL213 4.4 24.9 1.0
N B:VAL213 4.4 24.9 1.0
N B:VAL205 4.4 25.6 1.0
O B:CYS211 4.5 29.8 1.0
CA B:VAL213 4.6 24.0 1.0
N B:CYS211 4.6 30.5 1.0
CB B:VAL205 4.7 25.7 1.0
CA B:CYS211 4.8 30.8 1.0
C B:ALA204 4.8 28.1 1.0
N B:ASN208 4.8 26.4 1.0
C B:ALA206 4.8 26.9 1.0
CB B:CYS211 4.9 31.5 1.0
CB B:ASN208 4.9 29.1 1.0
CB B:ALA204 4.9 26.7 1.0
N B:ASN207 5.0 25.5 1.0

Calcium binding site 5 out of 18 in 4omd

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Calcium binding site 5 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:18.7
occ:1.00
 OD2 B:ASP301 2.2 16.1 1.0
OD1 B:ASP258 2.4 22.3 1.0
O B:HOH735 2.4 29.5 1.0
O B:HOH711 2.4 22.2 1.0
O B:HOH782 2.5 33.3 1.0
OE1 B:GLU331 2.5 20.4 1.0
OE2 B:GLU331 2.5 19.9 1.0
CD B:GLU331 2.9 19.3 1.0
CG B:ASP301 3.2 20.2 1.0
CG B:ASP258 3.5 23.7 1.0
OD1 B:ASP301 3.9 18.5 1.0
CB B:ASP301 4.1 19.3 1.0
CB B:ASP258 4.2 23.4 1.0
N34 I:00S5 4.2 19.6 1.0
CA B:ASP258 4.3 24.5 1.0
O B:HOH764 4.3 23.8 1.0
CG B:GLU331 4.4 19.8 1.0
O B:SER293 4.4 17.3 1.0
OD2 B:ASP258 4.4 22.0 1.0
OD2 B:ASP306 4.4 20.2 1.0
O B:SER302 4.5 26.3 1.0
CB B:ASP306 4.7 18.6 1.0
CA B:GLY294 4.7 20.1 1.0
CA B:CYS303 4.8 23.8 1.0
O B:GLU257 4.8 25.3 1.0
C27 I:00S5 4.8 18.6 1.0
C B:SER302 4.8 24.9 1.0
N B:GLY296 4.9 15.9 1.0
O B:PRO256 5.0 19.9 1.0

Calcium binding site 6 out of 18 in 4omd

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Calcium binding site 6 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca605

b:42.5
occ:1.00
 O B:HOH769 2.5 30.2 1.0
O B:ASP181 2.5 29.1 1.0
OD2 B:ASP174 2.6 23.5 1.0
OD1 B:ASP179 2.7 30.1 1.0
OD2 B:ASP179 2.7 35.8 1.0
CG B:ASP179 3.0 33.3 1.0
CG B:ASP174 3.6 24.7 1.0
C B:ASP181 3.6 29.7 1.0
CB B:ASP181 3.9 31.8 1.0
CB B:ASP174 3.9 25.2 1.0
CA B:ASP181 4.2 30.9 1.0
CG B:ASP181 4.3 34.2 1.0
OD1 B:ASP181 4.5 36.0 1.0
CB B:ASP179 4.5 29.9 1.0
N B:ASP181 4.6 31.4 1.0
O B:GLN183 4.7 26.4 1.0
NH2 B:ARG225 4.7 22.4 1.0
OD1 B:ASP174 4.7 23.1 1.0
N B:PRO182 4.8 29.3 1.0
OD2 B:ASP177 4.8 36.6 1.0
CB B:ASP177 4.8 34.0 1.0
OD2 B:ASP181 4.9 37.2 1.0
N B:GLN183 4.9 29.3 1.0

Calcium binding site 7 out of 18 in 4omd

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Calcium binding site 7 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca603

b:19.0
occ:1.00
 OD2 C:ASP115 2.2 30.8 1.0
O C:VAL210 2.3 23.1 1.0
OD1 C:ASP162 2.3 20.5 1.0
O C:VAL205 2.3 14.8 1.0
OD1 C:ASN208 2.4 21.1 1.0
O C:GLY212 2.4 22.1 1.0
OD2 C:ASP162 2.6 21.4 1.0
CG C:ASP162 2.8 20.6 1.0
CG C:ASN208 3.4 21.7 1.0
CG C:ASP115 3.4 24.9 1.0
C C:VAL210 3.5 23.6 1.0
C C:VAL205 3.5 16.0 1.0
C C:GLY212 3.6 21.0 1.0
ND2 C:ASN208 3.7 23.6 1.0
CA C:VAL210 4.2 23.0 1.0
CB C:ASP115 4.2 22.1 1.0
N C:GLY212 4.2 24.8 1.0
N C:VAL210 4.2 23.0 1.0
CB C:VAL210 4.2 21.9 1.0
OD1 C:ASP115 4.3 26.3 1.0
C C:CYS211 4.3 26.6 1.0
CB C:ASP162 4.3 20.9 1.0
CA C:VAL205 4.4 16.2 1.0
N C:ALA206 4.4 16.7 1.0
CA C:GLY212 4.4 22.8 1.0
CA C:ALA206 4.4 20.3 1.0
N C:VAL205 4.4 18.5 1.0
O C:HOH715 4.5 5.0 1.0
N C:CYS211 4.5 25.2 1.0
O C:CYS211 4.6 29.1 1.0
CG1 C:VAL213 4.6 17.0 1.0
N C:VAL213 4.6 19.9 1.0
CB C:VAL205 4.7 15.5 1.0
CB C:ASN208 4.7 19.9 1.0
CA C:VAL213 4.7 19.3 1.0
N C:ASN208 4.8 19.1 1.0
CG1 C:VAL210 4.8 18.6 1.0
CA C:CYS211 4.8 27.6 1.0
C C:ALA204 4.8 21.4 1.0
C C:ALA206 4.9 21.5 1.0
CB C:CYS211 4.9 29.8 1.0
N C:ASN207 5.0 20.2 1.0

Calcium binding site 8 out of 18 in 4omd

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Calcium binding site 8 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca604

b:20.4
occ:1.00
 OD2 C:ASP301 2.2 20.9 1.0
O C:HOH742 2.3 24.7 1.0
O C:HOH769 2.4 14.0 1.0
OE1 C:GLU331 2.4 17.1 1.0
OD1 C:ASP258 2.5 20.7 1.0
OE2 C:GLU331 2.5 20.0 1.0
O C:HOH725 2.6 11.3 1.0
CD C:GLU331 2.8 18.7 1.0
CG C:ASP301 3.2 21.6 1.0
CG C:ASP258 3.6 21.4 1.0
OD1 C:ASP301 3.9 15.6 1.0
O C:HOH794 4.1 28.7 1.0
CB C:ASP301 4.1 20.7 1.0
CB C:ASP258 4.2 20.9 1.0
N34 J:00S5 4.2 22.0 1.0
CG C:GLU331 4.3 17.6 1.0
O C:SER293 4.3 20.2 1.0
CA C:ASP258 4.3 23.0 1.0
O C:SER302 4.4 26.8 1.0
OD2 C:ASP258 4.5 22.9 1.0
O C:HOH767 4.5 19.2 1.0
OD2 C:ASP306 4.6 19.6 1.0
CA C:GLY294 4.7 18.3 1.0
CB C:ASP306 4.7 22.8 1.0
CA C:CYS303 4.7 23.4 1.0
C C:SER302 4.8 24.5 1.0
N C:GLY296 4.8 18.8 1.0
C27 J:00S5 4.9 21.6 1.0
O C:GLU257 4.9 22.9 1.0
N C:CYS303 5.0 23.6 1.0

Calcium binding site 9 out of 18 in 4omd

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Calcium binding site 9 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca605

b:33.6
occ:1.00
 OD1 C:ASP179 2.5 31.6 1.0
O C:ASP181 2.5 25.7 1.0
OD2 C:ASP174 2.5 27.5 1.0
O C:HOH773 2.6 32.0 1.0
OD2 C:ASP179 2.7 35.0 1.0
CG C:ASP179 3.0 30.7 1.0
CG C:ASP174 3.5 25.9 1.0
C C:ASP181 3.6 25.0 1.0
CB C:ASP174 3.7 25.4 1.0
CB C:ASP181 3.9 28.3 1.0
CA C:ASP181 4.2 26.1 1.0
CB C:ASP179 4.5 29.2 1.0
N C:ASP181 4.5 25.7 1.0
CG C:ASP181 4.5 31.0 1.0
OD1 C:ASP174 4.6 26.2 1.0
NH2 C:ARG225 4.7 16.9 1.0
OD2 C:ASP177 4.7 33.9 1.0
CB C:ASP177 4.7 32.7 1.0
N C:PRO182 4.7 23.3 1.0
OD1 C:ASP181 4.8 34.1 1.0
O C:GLN183 4.8 22.7 1.0
N C:GLN183 4.9 23.6 1.0

Calcium binding site 10 out of 18 in 4omd

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Calcium binding site 10 out of 18 in the X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of X-Ray Structure of Human Furin in Complex with the Competitive Inhibitor Phac-Rvr-Amba within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca603

b:30.9
occ:1.00
 OD2 D:ASP115 2.2 30.1 1.0
O D:VAL205 2.2 20.3 1.0
OD1 D:ASP162 2.3 23.8 1.0
O D:VAL210 2.4 26.6 1.0
O D:GLY212 2.4 23.4 1.0
OD1 D:ASN208 2.5 19.3 1.0
OD2 D:ASP162 2.7 22.6 1.0
CG D:ASP162 2.9 21.4 1.0
C D:VAL205 3.4 21.7 1.0
CG D:ASP115 3.5 29.2 1.0
CG D:ASN208 3.5 24.0 1.0
C D:VAL210 3.6 27.8 1.0
C D:GLY212 3.7 24.1 1.0
ND2 D:ASN208 3.9 21.1 1.0
CA D:VAL210 4.3 27.1 1.0
CB D:ASP115 4.3 27.8 1.0
N D:VAL210 4.3 28.6 1.0
CA D:VAL205 4.3 20.1 1.0
N D:ALA206 4.3 22.0 1.0
N D:GLY212 4.3 29.0 1.0
CB D:VAL210 4.3 25.1 1.0
CA D:ALA206 4.4 22.3 1.0
OD1 D:ASP115 4.4 29.2 1.0
CB D:ASP162 4.4 19.7 1.0
N D:VAL205 4.4 20.9 1.0
C D:CYS211 4.4 32.0 1.0
CA D:GLY212 4.5 25.1 1.0
CB D:VAL205 4.5 15.5 1.0
CG1 D:VAL213 4.6 20.7 1.0
N D:VAL213 4.6 23.7 1.0
O D:CYS211 4.6 33.3 1.0
N D:CYS211 4.6 30.6 1.0
O D:HOH778 4.7 10.3 1.0
CA D:VAL213 4.7 21.9 1.0
CB D:ASN208 4.7 22.7 1.0
N D:ASN208 4.7 24.7 1.0
C D:ALA204 4.8 20.3 1.0
C D:ALA206 4.8 21.6 1.0
CG1 D:VAL210 4.9 23.8 1.0
CA D:CYS211 4.9 32.6 1.0
N D:ASN207 4.9 21.3 1.0
CB D:ALA204 5.0 17.0 1.0
CB D:CYS211 5.0 33.9 1.0

Reference:

S.O.Dahms, K.Hardes, G.L.Becker, T.Steinmetzer, H.Brandstetter, M.E.Than. X-Ray Structures of Human Furin in Complex with Competitive Inhibitors. Acs Chem.Biol. V. 9 1113 2014.
ISSN: ISSN 1554-8929
PubMed: 24666235
DOI: 10.1021/CB500087X
Page generated: Sun Jul 14 11:25:21 2024

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