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Fluorine in PDB 4if4: Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus

Protein crystallography data

The structure of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus, PDB code: 4if4 was solved by P.G.Leonard, A.M.Stock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.98 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 110.603, 110.603, 284.292, 90.00, 90.00, 120.00
R / Rfree (%) 18.1 / 22.6

Other elements in 4if4:

The structure of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus (pdb code 4if4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus, PDB code: 4if4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 4if4

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Fluorine binding site 1 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


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Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:34.4
occ:1.00
F1 A:BEF301 0.0 34.4 1.0
BE A:BEF301 1.5 35.2 1.0
F2 A:BEF301 2.5 33.7 1.0
OD1 A:ASP55 2.5 37.5 1.0
F3 A:BEF301 2.6 39.7 1.0
O A:HOH419 2.8 38.5 1.0
NZ A:LYS105 2.9 37.0 1.0
N A:SER84 3.1 27.8 1.0
OG A:SER84 3.2 60.4 1.0
OG1 A:THR83 3.4 35.2 1.0
CA A:THR83 3.4 29.7 1.0
CE A:LYS105 3.5 30.7 1.0
CG A:ASP55 3.7 41.8 1.0
C A:THR83 3.7 37.0 1.0
CD A:LYS105 3.8 37.4 1.0
O A:HOH427 3.8 28.3 1.0
CB A:THR83 3.9 34.0 1.0
CB A:SER84 3.9 41.7 1.0
CA A:SER84 4.1 40.0 1.0
CE2 A:PHE85 4.2 46.8 1.0
OD2 A:ASP55 4.2 37.9 1.0
MG A:MG300 4.2 36.6 1.0
CD2 A:PHE85 4.2 50.5 1.0
O A:LEU82 4.3 33.4 1.0
O A:HOH443 4.4 35.3 1.0
N A:THR83 4.6 33.6 1.0
N A:LEU56 4.7 34.6 1.0
OD2 A:ASP9 4.7 35.7 1.0
O A:THR83 4.9 36.5 1.0
CB A:ASP55 4.9 33.6 1.0
CG A:LYS105 4.9 29.0 1.0
C A:LEU82 4.9 35.8 1.0
N A:PHE85 5.0 32.7 1.0

Fluorine binding site 2 out of 12 in 4if4

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Fluorine binding site 2 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:33.7
occ:1.00
F2 A:BEF301 0.0 33.7 1.0
BE A:BEF301 1.6 35.2 1.0
OD1 A:ASP55 2.5 37.5 1.0
F1 A:BEF301 2.5 34.4 1.0
F3 A:BEF301 2.5 39.7 1.0
OG1 A:THR83 2.6 35.2 1.0
N A:LEU57 2.8 33.1 1.0
N A:LEU56 2.8 34.6 1.0
CB A:LEU56 3.2 30.4 1.0
CA A:LEU56 3.3 38.8 1.0
CB A:THR83 3.4 34.0 1.0
CG A:ASP55 3.5 41.8 1.0
C A:LEU56 3.5 40.9 1.0
CD2 A:PHE85 3.5 50.5 1.0
CE2 A:PHE85 3.8 46.8 1.0
CA A:LEU57 3.9 34.7 1.0
CA A:THR83 3.9 29.7 1.0
C A:ASP55 4.0 35.1 1.0
CB A:LEU57 4.0 36.1 1.0
OD2 A:ASP55 4.1 37.9 1.0
MG A:MG300 4.2 36.6 1.0
N A:SER84 4.3 27.8 1.0
CA A:ASP55 4.4 33.4 1.0
O A:LEU57 4.5 34.7 1.0
CG A:LEU56 4.5 33.5 1.0
CB A:ASP55 4.6 33.6 1.0
O A:HOH419 4.6 38.5 1.0
O A:LEU82 4.7 33.4 1.0
C A:LEU57 4.7 32.8 1.0
C A:THR83 4.7 37.0 1.0
CG A:PHE85 4.7 45.6 1.0
O A:LEU56 4.7 43.3 1.0
CG2 A:THR83 4.8 35.8 1.0
CD2 A:LEU56 4.9 32.7 1.0
NZ A:LYS105 5.0 37.0 1.0

Fluorine binding site 3 out of 12 in 4if4

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Fluorine binding site 3 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F301

b:39.7
occ:1.00
F3 A:BEF301 0.0 39.7 1.0
BE A:BEF301 1.6 35.2 1.0
MG A:MG300 1.9 36.6 1.0
F2 A:BEF301 2.5 33.7 1.0
OD1 A:ASP55 2.6 37.5 1.0
F1 A:BEF301 2.6 34.4 1.0
OD2 A:ASP55 2.8 37.9 1.0
O A:HOH427 2.8 28.3 1.0
O A:HOH447 2.9 35.3 1.0
O A:LEU57 3.0 34.7 1.0
CG A:ASP55 3.0 41.8 1.0
O A:HOH419 3.3 38.5 1.0
N A:LEU57 3.4 33.1 1.0
CB A:LEU57 3.5 36.1 1.0
CA A:LEU57 3.7 34.7 1.0
C A:LEU57 3.8 32.8 1.0
O A:HOH449 3.8 42.6 1.0
CE2 A:PHE85 3.9 46.8 1.0
OD1 A:ASP10 4.1 51.8 1.0
NZ A:LYS105 4.2 37.0 1.0
N A:LEU56 4.4 34.6 1.0
C A:LEU56 4.5 40.9 1.0
CD2 A:PHE85 4.5 50.5 1.0
CB A:ASP55 4.5 33.6 1.0
CG A:LEU57 4.5 63.4 1.0
CD2 A:LEU57 4.8 44.2 1.0
OG1 A:THR83 4.9 35.2 1.0
CA A:LEU56 4.9 38.8 1.0
CZ A:PHE85 5.0 49.0 1.0
OD2 A:ASP9 5.0 35.7 1.0

Fluorine binding site 4 out of 12 in 4if4

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Fluorine binding site 4 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:35.9
occ:1.00
F1 B:BEF301 0.0 35.9 1.0
BE B:BEF301 1.5 32.6 1.0
OD2 B:ASP55 2.4 35.4 1.0
F2 B:BEF301 2.5 30.7 1.0
F3 B:BEF301 2.5 39.1 1.0
OG1 B:THR83 2.6 33.7 1.0
N B:LEU57 2.8 36.8 1.0
N B:LEU56 2.9 34.4 1.0
CB B:LEU56 3.2 31.7 1.0
CA B:LEU56 3.3 37.1 1.0
CB B:THR83 3.3 30.9 1.0
C B:LEU56 3.5 41.8 1.0
CG B:ASP55 3.5 41.9 1.0
CD2 B:PHE85 3.5 49.1 1.0
CE2 B:PHE85 3.8 52.9 1.0
CA B:THR83 3.9 29.0 1.0
CA B:LEU57 3.9 35.8 1.0
CB B:LEU57 4.0 38.7 1.0
C B:ASP55 4.0 34.0 1.0
OD1 B:ASP55 4.0 40.6 1.0
CG B:LEU56 4.1 45.5 1.0
MG B:MG300 4.2 37.4 1.0
N B:SER84 4.2 35.8 1.0
CA B:ASP55 4.4 29.8 1.0
O B:LEU57 4.5 33.4 1.0
CB B:ASP55 4.6 31.4 1.0
C B:THR83 4.6 38.4 1.0
C B:LEU57 4.6 37.3 1.0
O B:HOH415 4.6 43.0 1.0
O B:LEU82 4.7 35.3 1.0
O B:LEU56 4.7 44.8 1.0
CG2 B:THR83 4.7 38.0 1.0
CG B:PHE85 4.8 45.0 1.0
NZ B:LYS105 4.8 35.8 1.0
OG B:SER84 4.9 62.8 1.0

Fluorine binding site 5 out of 12 in 4if4

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Fluorine binding site 5 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:30.7
occ:1.00
F2 B:BEF301 0.0 30.7 1.0
BE B:BEF301 1.6 32.6 1.0
F1 B:BEF301 2.5 35.9 1.0
F3 B:BEF301 2.5 39.1 1.0
OD2 B:ASP55 2.6 35.4 1.0
NZ B:LYS105 2.7 35.8 1.0
O B:HOH415 2.8 43.0 1.0
N B:SER84 3.1 35.8 1.0
OG1 B:THR83 3.4 33.7 1.0
CA B:THR83 3.4 29.0 1.0
CE B:LYS105 3.5 29.3 1.0
OG B:SER84 3.5 62.8 1.0
C B:THR83 3.7 38.4 1.0
CG B:ASP55 3.7 41.9 1.0
CD B:LYS105 3.8 39.9 1.0
O B:HOH420 3.8 28.3 1.0
CB B:THR83 3.9 30.9 1.0
CB B:SER84 3.9 46.9 1.0
CA B:SER84 4.1 43.2 1.0
MG B:MG300 4.1 37.4 1.0
CE2 B:PHE85 4.2 52.9 1.0
OD1 B:ASP55 4.2 40.6 1.0
CD2 B:PHE85 4.3 49.1 1.0
O B:LEU82 4.3 35.3 1.0
O B:HOH433 4.4 30.9 1.0
N B:THR83 4.6 30.6 1.0
OD2 B:ASP9 4.7 35.1 1.0
N B:LEU56 4.7 34.4 1.0
O B:THR83 4.8 39.2 1.0
CG B:LYS105 4.9 33.4 1.0
CB B:ASP55 4.9 31.4 1.0
C B:LEU82 4.9 33.4 1.0
N B:LEU57 5.0 36.8 1.0
O B:HOH436 5.0 44.3 1.0
N B:PHE85 5.0 37.5 1.0

Fluorine binding site 6 out of 12 in 4if4

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Fluorine binding site 6 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F301

b:39.1
occ:1.00
F3 B:BEF301 0.0 39.1 1.0
BE B:BEF301 1.6 32.6 1.0
MG B:MG300 1.9 37.4 1.0
F2 B:BEF301 2.5 30.7 1.0
F1 B:BEF301 2.5 35.9 1.0
OD2 B:ASP55 2.6 35.4 1.0
OD1 B:ASP55 2.8 40.6 1.0
O B:HOH420 2.8 28.3 1.0
O B:HOH425 2.9 38.1 1.0
O B:LEU57 3.0 33.4 1.0
CG B:ASP55 3.0 41.9 1.0
O B:HOH415 3.2 43.0 1.0
N B:LEU57 3.5 36.8 1.0
CB B:LEU57 3.5 38.7 1.0
CA B:LEU57 3.7 35.8 1.0
O B:HOH436 3.7 44.3 1.0
C B:LEU57 3.8 37.3 1.0
CE2 B:PHE85 3.9 52.9 1.0
OD1 B:ASP10 4.0 51.4 1.0
NZ B:LYS105 4.1 35.8 1.0
N B:LEU56 4.4 34.4 1.0
C B:LEU56 4.5 41.8 1.0
CG B:LEU57 4.6 61.0 1.0
CD2 B:PHE85 4.6 49.1 1.0
CB B:ASP55 4.6 31.4 1.0
OG1 B:THR83 4.8 33.7 1.0
CZ B:PHE85 4.9 52.6 1.0
CD2 B:LEU57 4.9 47.1 1.0
OD2 B:ASP9 4.9 35.1 1.0
CA B:LEU56 5.0 37.1 1.0
OG B:SER84 5.0 62.8 1.0

Fluorine binding site 7 out of 12 in 4if4

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Fluorine binding site 7 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:40.8
occ:1.00
F1 C:BEF301 0.0 40.8 1.0
BE C:BEF301 1.5 44.4 1.0
OD1 C:ASP55 2.3 35.0 1.0
F2 C:BEF301 2.6 40.2 1.0
F3 C:BEF301 2.6 42.6 1.0
N C:LEU56 2.7 37.7 1.0
OG1 C:THR83 2.7 46.6 1.0
N C:LEU57 2.7 38.5 1.0
CB C:LEU56 3.1 42.7 1.0
CA C:LEU56 3.2 36.9 1.0
CG C:ASP55 3.3 39.9 1.0
C C:LEU56 3.4 46.0 1.0
CB C:THR83 3.4 49.1 1.0
C C:ASP55 3.8 42.8 1.0
CD2 C:PHE85 3.8 45.6 1.0
CA C:LEU57 3.8 39.5 1.0
OD2 C:ASP55 3.9 41.9 1.0
CE2 C:PHE85 3.9 49.0 1.0
CB C:LEU57 4.0 33.1 1.0
CA C:THR83 4.0 38.1 1.0
MG C:MG300 4.0 48.4 1.0
CA C:ASP55 4.1 40.0 1.0
O C:LEU57 4.3 47.0 1.0
CB C:ASP55 4.3 30.9 1.0
N C:SER84 4.5 33.3 1.0
C C:LEU57 4.5 46.5 1.0
CG C:LEU56 4.5 47.4 1.0
O C:LEU82 4.5 40.2 1.0
O C:LEU56 4.6 40.9 1.0
O C:HOH426 4.6 37.2 1.0
CG2 C:THR83 4.8 42.7 1.0
O C:ASP55 4.8 46.5 1.0
C C:THR83 4.8 41.7 1.0
OG C:SER84 4.9 56.9 1.0
O C:HOH418 4.9 36.8 1.0
NZ C:LYS105 4.9 38.2 1.0
CD2 C:LEU56 4.9 46.6 1.0

Fluorine binding site 8 out of 12 in 4if4

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Fluorine binding site 8 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:40.2
occ:1.00
F2 C:BEF301 0.0 40.2 1.0
BE C:BEF301 1.6 44.4 1.0
OD1 C:ASP55 2.5 35.0 1.0
F3 C:BEF301 2.5 42.6 1.0
F1 C:BEF301 2.6 40.8 1.0
NZ C:LYS105 2.7 38.2 1.0
O C:HOH426 2.8 37.2 1.0
CE C:LYS105 3.3 38.0 1.0
N C:SER84 3.4 33.3 1.0
OG C:SER84 3.4 56.9 1.0
OG1 C:THR83 3.5 46.6 1.0
CA C:THR83 3.5 38.1 1.0
CG C:ASP55 3.6 39.9 1.0
O C:HOH418 3.6 36.8 1.0
CD C:LYS105 3.8 37.4 1.0
C C:THR83 3.9 41.7 1.0
CB C:THR83 3.9 49.1 1.0
MG C:MG300 4.0 48.4 1.0
OD2 C:ASP55 4.1 41.9 1.0
CB C:SER84 4.3 48.3 1.0
O C:LEU82 4.3 40.2 1.0
O C:HOH425 4.3 36.8 1.0
CE2 C:PHE85 4.3 49.0 1.0
CA C:SER84 4.4 37.4 1.0
OD2 C:ASP9 4.4 44.5 1.0
CD2 C:PHE85 4.6 45.6 1.0
N C:THR83 4.7 39.7 1.0
N C:LEU56 4.7 37.7 1.0
CG C:LYS105 4.8 38.6 1.0
CB C:ASP55 4.8 30.9 1.0
O C:HOH412 4.9 35.9 1.0
O C:HOH422 4.9 39.3 1.0
C C:LEU82 4.9 41.7 1.0

Fluorine binding site 9 out of 12 in 4if4

Go back to Fluorine Binding Sites List in 4if4
Fluorine binding site 9 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:42.6
occ:1.00
F3 C:BEF301 0.0 42.6 1.0
BE C:BEF301 1.6 44.4 1.0
MG C:MG300 1.8 48.4 1.0
OD1 C:ASP55 2.5 35.0 1.0
F2 C:BEF301 2.5 40.2 1.0
F1 C:BEF301 2.6 40.8 1.0
O C:HOH418 2.7 36.8 1.0
OD2 C:ASP55 2.7 41.9 1.0
O C:HOH412 2.7 35.9 1.0
O C:LEU57 2.9 47.0 1.0
CG C:ASP55 3.0 39.9 1.0
O C:HOH426 3.2 37.2 1.0
N C:LEU57 3.7 38.5 1.0
O C:HOH422 3.7 39.3 1.0
CB C:LEU57 3.7 33.1 1.0
C C:LEU57 3.8 46.5 1.0
CA C:LEU57 3.9 39.5 1.0
OD1 C:ASP10 3.9 49.9 1.0
CE2 C:PHE85 4.0 49.0 1.0
NZ C:LYS105 4.2 38.2 1.0
CG C:LEU57 4.4 60.7 1.0
CB C:ASP55 4.5 30.9 1.0
N C:LEU56 4.5 37.7 1.0
C C:LEU56 4.6 46.0 1.0
CD2 C:LEU57 4.7 41.5 1.0
CD2 C:PHE85 4.7 45.6 1.0
OG C:SER84 4.8 56.9 1.0
OD2 C:ASP9 4.9 44.5 1.0
OG1 C:THR83 4.9 46.6 1.0
CG C:ASP10 4.9 47.1 1.0
CZ C:PHE85 4.9 49.0 1.0

Fluorine binding site 10 out of 12 in 4if4

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Fluorine binding site 10 out of 12 in the Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Magnesium and Beryllofluoride-Activated Vrar From Staphylococcus Aureus within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F301

b:46.0
occ:1.00
F1 D:BEF301 0.0 46.0 1.0
BE D:BEF301 1.5 44.7 1.0
OD1 D:ASP55 2.4 37.2 1.0
F2 D:BEF301 2.6 37.0 1.0
F3 D:BEF301 2.6 43.8 1.0
OG1 D:THR83 2.6 48.3 1.0
N D:LEU56 2.7 38.4 1.0
N D:LEU57 2.8 40.0 1.0
CB D:LEU56 3.1 39.4 1.0
CA D:LEU56 3.2 32.7 1.0
CG D:ASP55 3.3 42.0 1.0
CB D:THR83 3.3 46.2 1.0
C D:LEU56 3.4 44.1 1.0
CD2 D:PHE85 3.7 45.0 1.0
C D:ASP55 3.8 44.0 1.0
CE2 D:PHE85 3.8 51.3 1.0
CA D:LEU57 3.9 40.2 1.0
OD2 D:ASP55 3.9 39.8 1.0
CB D:LEU57 4.0 32.4 1.0
CA D:THR83 4.0 41.5 1.0
MG D:MG300 4.1 51.6 1.0
CA D:ASP55 4.2 40.8 1.0
O D:LEU57 4.3 46.9 1.0
CB D:ASP55 4.4 38.9 1.0
N D:SER84 4.5 33.1 1.0
CG D:LEU56 4.5 48.8 1.0
C D:LEU57 4.5 44.1 1.0
O D:LEU82 4.6 43.3 1.0
O D:LEU56 4.6 43.6 1.0
O D:HOH424 4.7 36.4 1.0
CG2 D:THR83 4.7 38.8 1.0
C D:THR83 4.8 42.5 1.0
O D:ASP55 4.8 43.8 1.0
O D:HOH426 4.9 41.1 1.0
NZ D:LYS105 4.9 33.1 1.0
CG D:PHE85 4.9 49.1 1.0
CD2 D:LEU56 5.0 49.5 1.0
OG D:SER84 5.0 56.0 1.0

Reference:

P.G.Leonard, D.Golemi-Kotra, A.M.Stock. Phosphorylation-Dependent Conformational Changes and Domain Rearrangements in Staphylococcus Aureus Vrar Activation. Proc.Natl.Acad.Sci.Usa V. 110 8525 2013.
ISSN: ISSN 0027-8424
PubMed: 23650349
DOI: 10.1073/PNAS.1302819110
Page generated: Sun Dec 13 12:04:26 2020

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