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Fluorine in PDB 5g1a: Bordetella Alcaligenes Hdah Bound to Pfsaha

Enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha

All present enzymatic activity of Bordetella Alcaligenes Hdah Bound to Pfsaha:
3.5.1.4;

Protein crystallography data

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha, PDB code: 5g1a was solved by A.Kraemer, F.J.Meyer-Almes, O.Yildiz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.96 / 1.42
Space group P 42 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.440, 101.440, 175.930, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17

Other elements in 5g1a:

The structure of Bordetella Alcaligenes Hdah Bound to Pfsaha also contains other interesting chemical elements:

Potassium (K) 4 atoms
Zinc (Zn) 2 atoms

Fluorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Fluorine atom in the Bordetella Alcaligenes Hdah Bound to Pfsaha (pdb code 5g1a). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 24 binding sites of Fluorine where determined in the Bordetella Alcaligenes Hdah Bound to Pfsaha, PDB code: 5g1a:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 24 in 5g1a

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Fluorine binding site 1 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:20.6
occ:0.70
F A:7H1373 0.0 20.6 0.7
C1 A:7H1373 1.3 18.8 0.7
F1 A:7H1373 2.1 23.6 0.7
C A:7H1373 2.3 17.0 0.7
C2 A:7H1373 2.3 20.9 0.7
N A:7H1373 2.5 14.3 0.7
F3 A:7H1373 2.6 23.2 0.7
F7 A:7H1373 2.7 23.7 0.7
F6 A:7H1373 2.8 22.0 0.7
C4 A:7H1373 3.0 21.1 0.7
C3 A:7H1373 3.0 20.7 0.7
O A:GLY151 3.0 13.9 1.0
O A:HOH2276 3.1 36.3 1.0
CD2 A:HIS143 3.3 15.4 1.0
F2 A:7H1373 3.4 22.1 0.7
O1 A:7H1373 3.4 15.0 0.7
NE2 A:HIS143 3.5 17.1 1.0
F4 A:7H1373 3.6 22.4 0.7
C A:GLY151 3.7 14.6 1.0
O A:7H1373 3.8 13.5 0.7
CA A:GLY151 3.8 15.9 1.0
CD2 A:PHE152 4.0 17.9 0.5
F5 A:7H1373 4.1 24.6 0.7
O A:HOH2414 4.3 33.2 1.0
OH A:TYR312 4.3 15.6 1.0
CD2 A:PHE152 4.4 13.5 0.5
CE2 A:PHE152 4.4 18.8 0.5
C5 A:7H1373 4.5 23.9 0.7
CG A:HIS143 4.6 13.6 1.0
CD2 A:PHE208 4.6 15.1 1.0
CE1 A:HIS143 4.8 15.4 1.0
CG A:PHE152 4.8 18.2 0.5
CE2 A:PHE208 4.8 16.0 1.0
F10 A:7H1373 4.8 29.4 0.7
N A:PHE152 4.8 14.6 0.5
N A:PHE152 4.8 14.2 0.5
CE2 A:PHE152 4.9 14.3 0.5

Fluorine binding site 2 out of 24 in 5g1a

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Fluorine binding site 2 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:23.6
occ:0.70
F1 A:7H1373 0.0 23.6 0.7
C1 A:7H1373 1.3 18.8 0.7
F A:7H1373 2.1 20.6 0.7
C2 A:7H1373 2.3 20.9 0.7
C A:7H1373 2.4 17.0 0.7
F2 A:7H1373 2.7 22.1 0.7
F4 A:7H1373 2.8 22.4 0.7
OH A:TYR312 2.8 15.6 1.0
O1 A:7H1373 2.9 15.0 0.7
C3 A:7H1373 2.9 20.7 0.7
F7 A:7H1373 3.1 23.7 0.7
CD2 A:PHE152 3.3 17.9 0.5
O A:HOH2414 3.3 33.2 1.0
CE2 A:PHE152 3.4 18.8 0.5
N A:7H1373 3.4 14.3 0.7
F3 A:7H1373 3.4 23.2 0.7
CZ A:TYR312 3.5 12.1 1.0
C4 A:7H1373 3.6 21.1 0.7
O A:HOH2276 3.7 36.3 1.0
CD2 A:PHE152 3.8 13.5 0.5
CE2 A:TYR312 4.0 11.6 1.0
F6 A:7H1373 4.1 22.0 0.7
CE2 A:PHE152 4.1 14.3 0.5
F5 A:7H1373 4.1 24.6 0.7
CE1 A:TYR312 4.2 12.4 1.0
O A:GLY151 4.3 13.9 1.0
CD1 A:LEU275 4.5 10.9 1.0
CG A:PHE152 4.5 18.2 0.5
O A:7H1373 4.6 13.5 0.7
CZ A:PHE152 4.7 19.5 0.5
CG A:PHE152 4.9 14.8 0.5
C5 A:7H1373 5.0 23.9 0.7
C A:GLY151 5.0 14.6 1.0
ZN A:ZN370 5.0 10.9 0.5

Fluorine binding site 3 out of 24 in 5g1a

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Fluorine binding site 3 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:22.1
occ:0.70
F2 A:7H1373 0.0 22.1 0.7
C2 A:7H1373 1.3 20.9 0.7
F3 A:7H1373 2.1 23.2 0.7
C1 A:7H1373 2.3 18.8 0.7
C3 A:7H1373 2.3 20.7 0.7
F4 A:7H1373 2.6 22.4 0.7
F5 A:7H1373 2.6 24.6 0.7
F1 A:7H1373 2.7 23.6 0.7
C A:7H1373 2.8 17.0 0.7
CE1 A:HIS182 3.0 10.2 1.0
NE2 A:HIS182 3.3 10.2 1.0
O1 A:7H1373 3.4 15.0 0.7
F A:7H1373 3.4 20.6 0.7
ND1 A:HIS182 3.5 9.8 1.0
N A:7H1373 3.6 14.3 0.7
CD1 A:LEU275 3.7 10.9 1.0
C4 A:7H1373 3.7 21.1 0.7
CD2 A:HIS182 3.9 9.6 1.0
CG A:HIS182 4.0 8.8 1.0
F6 A:7H1373 4.1 22.0 0.7
CB A:LEU275 4.1 8.6 1.0
CD2 A:LEU275 4.2 10.7 1.0
F7 A:7H1373 4.2 23.7 0.7
CG A:LEU275 4.2 10.5 1.0
CE2 A:TYR312 4.2 11.6 1.0
OH A:TYR312 4.5 15.6 1.0
ZN A:ZN370 4.6 10.9 0.5
CZ A:TYR312 4.6 12.1 1.0
O A:7H1373 4.7 13.5 0.7
O A:LEU275 4.8 9.7 1.0
C5 A:7H1373 4.8 23.9 0.7
F8 A:7H1373 4.9 26.2 0.7
CB A:PHE208 5.0 11.9 1.0

Fluorine binding site 4 out of 24 in 5g1a

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Fluorine binding site 4 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:23.2
occ:0.70
F3 A:7H1373 0.0 23.2 0.7
C2 A:7H1373 1.3 20.9 0.7
F2 A:7H1373 2.1 22.1 0.7
C1 A:7H1373 2.3 18.8 0.7
C3 A:7H1373 2.3 20.7 0.7
F A:7H1373 2.6 20.6 0.7
F5 A:7H1373 2.6 24.6 0.7
F6 A:7H1373 2.7 22.0 0.7
N A:7H1373 2.8 14.3 0.7
C A:7H1373 2.8 17.0 0.7
C4 A:7H1373 3.1 21.1 0.7
CD2 A:PHE208 3.3 15.1 1.0
F1 A:7H1373 3.4 23.6 0.7
F4 A:7H1373 3.4 22.4 0.7
CG A:HIS182 3.5 8.8 1.0
CB A:PHE208 3.5 11.9 1.0
CG A:PHE208 3.5 14.7 1.0
ND1 A:HIS182 3.6 9.8 1.0
CD2 A:HIS182 3.6 9.6 1.0
NE2 A:HIS143 3.6 17.1 1.0
NE2 A:HIS182 3.7 10.2 1.0
CE1 A:HIS182 3.8 10.2 1.0
F7 A:7H1373 3.8 23.7 0.7
O1 A:7H1373 3.9 15.0 0.7
O A:7H1373 4.0 13.5 0.7
CB A:HIS182 4.1 8.1 1.0
CE2 A:PHE208 4.2 16.0 1.0
F9 A:7H1373 4.2 27.3 0.7
C5 A:7H1373 4.3 23.9 0.7
CD2 A:HIS143 4.3 15.4 1.0
CE1 A:HIS143 4.5 15.4 1.0
CD1 A:PHE208 4.5 15.8 1.0
ZN A:ZN370 4.7 10.9 0.5
CA A:PHE208 4.9 10.8 1.0
F8 A:7H1373 4.9 26.2 0.7

Fluorine binding site 5 out of 24 in 5g1a

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Fluorine binding site 5 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:22.4
occ:0.70
F4 A:7H1373 0.0 22.4 0.7
C3 A:7H1373 1.3 20.7 0.7
F5 A:7H1373 2.1 24.6 0.7
C2 A:7H1373 2.3 20.9 0.7
C4 A:7H1373 2.3 21.1 0.7
F2 A:7H1373 2.6 22.1 0.7
F7 A:7H1373 2.6 23.7 0.7
F8 A:7H1373 2.7 26.2 0.7
F1 A:7H1373 2.8 23.6 0.7
C1 A:7H1373 3.0 18.8 0.7
C5 A:7H1373 3.1 23.9 0.7
CE2 A:PHE152 3.4 18.8 0.5
F3 A:7H1373 3.4 23.2 0.7
F6 A:7H1373 3.5 22.0 0.7
CD1 A:LEU21 3.6 16.9 1.0
F A:7H1373 3.6 20.6 0.7
CD1 A:LEU275 3.8 10.9 1.0
F9 A:7H1373 3.8 27.3 0.7
CE2 A:PHE152 3.9 14.3 0.5
CZ A:PHE152 4.1 19.5 0.5
CD2 A:LEU275 4.2 10.7 1.0
CD2 A:PHE152 4.2 17.9 0.5
C6 A:7H1373 4.3 24.6 0.7
F11 A:7H1373 4.4 28.2 0.7
C A:7H1373 4.4 17.0 0.7
CD2 A:PHE152 4.4 13.5 0.5
CG A:LEU275 4.6 10.5 1.0
CG A:LEU21 4.7 15.7 1.0
CZ A:PHE152 4.9 15.4 0.5
CD2 A:LEU21 4.9 16.7 1.0
F10 A:7H1373 4.9 29.4 0.7

Fluorine binding site 6 out of 24 in 5g1a

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Fluorine binding site 6 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:24.6
occ:0.70
F5 A:7H1373 0.0 24.6 0.7
C3 A:7H1373 1.3 20.7 0.7
F4 A:7H1373 2.1 22.4 0.7
C2 A:7H1373 2.3 20.9 0.7
C4 A:7H1373 2.3 21.1 0.7
F2 A:7H1373 2.6 22.1 0.7
F3 A:7H1373 2.6 23.2 0.7
F9 A:7H1373 2.6 27.3 0.7
C5 A:7H1373 2.7 23.9 0.7
F8 A:7H1373 2.8 26.2 0.7
F6 A:7H1373 2.9 22.0 0.7
F7 A:7H1373 3.4 23.7 0.7
C1 A:7H1373 3.7 18.8 0.7
CG A:PHE208 3.9 14.7 1.0
CB A:PHE208 4.1 11.9 1.0
F1 A:7H1373 4.1 23.6 0.7
F A:7H1373 4.1 20.6 0.7
CD1 A:PHE208 4.2 15.8 1.0
C6 A:7H1373 4.3 24.6 0.7
CD2 A:LEU275 4.3 10.7 1.0
CD2 A:PHE208 4.4 15.1 1.0
NE2 A:HIS182 4.8 10.2 1.0
CE1 A:PHE208 4.8 17.3 1.0
F10 A:7H1373 4.8 29.4 0.7
C A:7H1373 4.9 17.0 0.7
CD1 A:LEU275 4.9 10.9 1.0
O2 A:7H1373 4.9 28.7 0.7
CD1 A:LEU21 4.9 16.9 1.0
F11 A:7H1373 4.9 28.2 0.7
CE2 A:PHE208 5.0 16.0 1.0

Fluorine binding site 7 out of 24 in 5g1a

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Fluorine binding site 7 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:22.0
occ:0.70
F6 A:7H1373 0.0 22.0 0.7
C4 A:7H1373 1.3 21.1 0.7
F7 A:7H1373 2.1 23.7 0.7
C5 A:7H1373 2.3 23.9 0.7
C3 A:7H1373 2.4 20.7 0.7
F9 A:7H1373 2.5 27.3 0.7
F10 A:7H1373 2.7 29.4 0.7
F3 A:7H1373 2.7 23.2 0.7
F A:7H1373 2.8 20.6 0.7
CE2 A:PHE208 2.8 16.0 1.0
C2 A:7H1373 2.9 20.9 0.7
CD2 A:PHE208 2.9 15.1 1.0
F5 A:7H1373 2.9 24.6 0.7
C6 A:7H1373 3.0 24.6 0.7
CZ A:PHE208 3.3 13.8 1.0
C1 A:7H1373 3.4 18.8 0.7
F8 A:7H1373 3.4 26.2 0.7
CG A:PHE208 3.4 14.7 1.0
F4 A:7H1373 3.5 22.4 0.7
CA A:GLY151 3.6 15.9 1.0
CE1 A:PHE208 3.7 17.3 1.0
CD1 A:PHE208 3.8 15.8 1.0
F11 A:7H1373 3.8 28.2 0.7
F1 A:7H1373 4.1 23.6 0.7
C7 A:7H1373 4.1 24.6 0.7
F2 A:7H1373 4.1 22.1 0.7
CD2 A:HIS143 4.3 15.4 1.0
NE2 A:HIS143 4.3 17.1 1.0
CB A:PHE208 4.4 11.9 1.0
C A:GLY151 4.4 14.6 1.0
O A:GLY151 4.5 13.9 1.0
N A:7H1373 4.6 14.3 0.7
C A:7H1373 4.6 17.0 0.7
O2 A:7H1373 4.7 28.7 0.7
N A:GLY151 4.7 16.2 1.0
N1 A:7H1373 4.7 22.9 0.7

Fluorine binding site 8 out of 24 in 5g1a

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Fluorine binding site 8 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:23.7
occ:0.70
F7 A:7H1373 0.0 23.7 0.7
C4 A:7H1373 1.3 21.1 0.7
F6 A:7H1373 2.1 22.0 0.7
C5 A:7H1373 2.3 23.9 0.7
C3 A:7H1373 2.3 20.7 0.7
F4 A:7H1373 2.6 22.4 0.7
F A:7H1373 2.7 20.6 0.7
C6 A:7H1373 2.8 24.6 0.7
F10 A:7H1373 2.8 29.4 0.7
F11 A:7H1373 2.8 28.2 0.7
F8 A:7H1373 2.9 26.2 0.7
CE2 A:PHE152 2.9 18.8 0.5
F1 A:7H1373 3.1 23.6 0.7
C2 A:7H1373 3.1 20.9 0.7
C1 A:7H1373 3.2 18.8 0.7
CE2 A:PHE152 3.2 14.3 0.5
CD2 A:PHE152 3.2 17.9 0.5
CD2 A:PHE152 3.3 13.5 0.5
F9 A:7H1373 3.4 27.3 0.7
CZ A:PHE152 3.4 19.5 0.5
F5 A:7H1373 3.4 24.6 0.7
CA A:GLY151 3.5 15.9 1.0
C A:GLY151 3.7 14.6 1.0
F3 A:7H1373 3.8 23.2 0.7
O A:GLY151 3.9 13.9 1.0
CG A:PHE152 3.9 18.2 0.5
CZ A:PHE152 4.0 15.4 0.5
CE1 A:PHE152 4.1 20.9 0.5
CG A:PHE152 4.1 14.8 0.5
F2 A:7H1373 4.2 22.1 0.7
CD1 A:PHE152 4.3 20.2 0.5
C7 A:7H1373 4.3 24.6 0.7
N A:PHE152 4.4 14.6 0.5
N A:PHE152 4.4 14.2 0.5
C A:7H1373 4.6 17.0 0.7
N A:GLY151 4.8 16.2 1.0
CE1 A:PHE152 4.8 16.2 0.5
CE2 A:PHE208 4.8 16.0 1.0
CD1 A:PHE152 4.8 16.3 0.5
O2 A:7H1373 4.8 28.7 0.7
CB A:PHE152 4.9 16.8 0.5
CB A:PHE152 4.9 14.7 0.5
CD1 A:LEU21 5.0 16.9 1.0

Fluorine binding site 9 out of 24 in 5g1a

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Fluorine binding site 9 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:26.2
occ:0.70
F8 A:7H1373 0.0 26.2 0.7
C5 A:7H1373 1.3 23.9 0.7
F9 A:7H1373 2.1 27.3 0.7
C6 A:7H1373 2.3 24.6 0.7
C4 A:7H1373 2.3 21.1 0.7
F11 A:7H1373 2.6 28.2 0.7
F4 A:7H1373 2.7 22.4 0.7
O2 A:7H1373 2.7 28.7 0.7
C3 A:7H1373 2.8 20.7 0.7
F5 A:7H1373 2.8 24.6 0.7
F7 A:7H1373 2.9 23.7 0.7
C7 A:7H1373 3.0 24.6 0.7
F6 A:7H1373 3.4 22.0 0.7
F10 A:7H1373 3.5 29.4 0.7
CD1 A:LEU21 3.5 16.9 1.0
CG A:LEU21 3.7 15.7 1.0
CD2 A:LEU21 3.9 16.7 1.0
CZ A:PHE152 4.2 19.5 0.5
C2 A:7H1373 4.3 20.9 0.7
N1 A:7H1373 4.3 22.9 0.7
CE2 A:PHE152 4.3 18.8 0.5
CE2 A:PHE152 4.4 14.3 0.5
CZ A:PHE152 4.6 15.4 0.5
CD1 A:ILE100 4.7 25.9 1.0
F3 A:7H1373 4.9 23.2 0.7
F2 A:7H1373 4.9 22.1 0.7

Fluorine binding site 10 out of 24 in 5g1a

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Fluorine binding site 10 out of 24 in the Bordetella Alcaligenes Hdah Bound to Pfsaha


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Bordetella Alcaligenes Hdah Bound to Pfsaha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F373

b:27.3
occ:0.70
F9 A:7H1373 0.0 27.3 0.7
C5 A:7H1373 1.3 23.9 0.7
F8 A:7H1373 2.1 26.2 0.7
C4 A:7H1373 2.3 21.1 0.7
C6 A:7H1373 2.3 24.6 0.7
F6 A:7H1373 2.5 22.0 0.7
C7 A:7H1373 2.6 24.6 0.7
O2 A:7H1373 2.6 28.7 0.7
F5 A:7H1373 2.6 24.6 0.7
F10 A:7H1373 2.9 29.4 0.7
CE1 A:PHE208 3.0 17.3 1.0
C3 A:7H1373 3.0 20.7 0.7
CD1 A:PHE208 3.1 15.8 1.0
CZ A:PHE208 3.4 13.8 1.0
F7 A:7H1373 3.4 23.7 0.7
F11 A:7H1373 3.4 28.2 0.7
N1 A:7H1373 3.6 22.9 0.7
CG A:PHE208 3.6 14.7 1.0
F4 A:7H1373 3.8 22.4 0.7
CE2 A:PHE208 3.9 16.0 1.0
CD2 A:PHE208 4.0 15.1 1.0
F3 A:7H1373 4.2 23.2 0.7
C2 A:7H1373 4.3 20.9 0.7
CB A:PHE208 4.5 11.9 1.0
C8 A:7H1373 4.5 25.1 0.7
C13 A:7H1373 4.8 27.8 0.7

Reference:

C.Meyners, A.Kramer, O.Yildiz, F.J.Meyer-Almes. The Thermodynamic Signature of Ligand Binding to Histone Deacetylase-Like Amidohydrolases Is Most Sensitive to the Flexibility in the L2-Loop Lining the Active Site Pocket. Biochim. Biophys. Acta V.1861 1855 2017.
ISSN: ISSN 0006-3002
PubMed: 28389333
DOI: 10.1016/J.BBAGEN.2017.04.001
Page generated: Sun Dec 13 12:22:51 2020

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