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Magnesium in PDB 3kr4: Structure of A Protease 3

Enzymatic activity of Structure of A Protease 3

All present enzymatic activity of Structure of A Protease 3:
3.4.11.1;

Protein crystallography data

The structure of Structure of A Protease 3, PDB code: 3kr4 was solved by S.Mcgowan, J.C.Whisstock, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.15 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 173.561, 178.121, 230.479, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 24.2

Other elements in 3kr4:

The structure of Structure of A Protease 3 also contains other interesting chemical elements:

Zinc (Zn) 12 atoms

Magnesium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Magnesium atom in the Structure of A Protease 3 (pdb code 3kr4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 12 binding sites of Magnesium where determined in the Structure of A Protease 3, PDB code: 3kr4:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 12 in 3kr4

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Magnesium binding site 1 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1004

b:24.9
occ:1.00
OD1 A:ASP459 1.8 12.2 1.0
OD2 A:ASP379 2.0 7.4 1.0
OE1 A:GLU461 2.2 9.4 1.0
O2 A:BES1003 2.3 20.1 1.0
O A:ASP459 2.5 11.2 1.0
CG A:ASP379 2.8 8.2 1.0
OD1 A:ASP379 2.9 9.1 1.0
CG A:ASP459 2.9 12.6 1.0
O3 A:BES1003 3.0 29.2 1.0
CD A:GLU461 3.2 11.1 1.0
C A:ASP459 3.2 10.2 1.0
ZN A:ZN1001 3.3 39.4 1.0
C2 A:BES1003 3.3 27.2 1.0
C3 A:BES1003 3.4 30.6 1.0
CA A:ASP459 3.4 10.5 1.0
OE2 A:GLU461 3.5 10.4 1.0
NZ A:LYS386 3.6 11.2 1.0
CB A:ASP459 3.7 10.5 1.0
CE A:LYS386 3.8 9.6 1.0
OD2 A:ASP459 3.8 16.4 1.0
C1 A:BES1003 3.9 26.0 1.0
CB A:ASP379 4.2 7.0 1.0
ND2 A:ASN432 4.3 7.9 1.0
N1 A:BES1003 4.4 33.2 1.0
N2 A:BES1003 4.4 20.1 1.0
CA A:GLY381 4.5 7.9 1.0
N A:ALA460 4.5 9.9 1.0
O2 A:CO31002 4.5 14.2 1.0
N A:GLU461 4.6 8.6 1.0
CG A:GLU461 4.6 9.2 1.0
N A:GLY381 4.7 7.8 1.0
N A:ASP459 4.8 9.2 1.0
OD2 A:ASP399 4.9 12.5 1.0
O A:THR458 5.0 9.2 1.0
CA A:ALA460 5.0 10.0 1.0

Magnesium binding site 2 out of 12 in 3kr4

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Magnesium binding site 2 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg1004

b:16.5
occ:1.00
OD1 B:ASP459 2.0 11.1 1.0
OD2 B:ASP379 2.1 8.5 1.0
O2 B:BES1003 2.1 19.9 1.0
OE1 B:GLU461 2.2 12.4 1.0
O B:ASP459 2.3 10.6 1.0
CG B:ASP379 2.9 9.6 1.0
CG B:ASP459 3.0 11.1 1.0
C2 B:BES1003 3.1 25.7 1.0
OD1 B:ASP379 3.1 7.7 1.0
C B:ASP459 3.1 10.0 1.0
O3 B:BES1003 3.1 30.4 1.0
CD B:GLU461 3.1 11.2 1.0
ZN B:ZN1001 3.2 37.6 1.0
C3 B:BES1003 3.2 29.2 1.0
CA B:ASP459 3.4 8.6 1.0
OE2 B:GLU461 3.4 11.8 1.0
C1 B:BES1003 3.8 24.0 1.0
CB B:ASP459 3.8 8.5 1.0
NZ B:LYS386 3.9 10.3 1.0
OD2 B:ASP459 4.0 12.8 1.0
CE B:LYS386 4.0 7.6 1.0
N2 B:BES1003 4.2 17.6 1.0
N1 B:BES1003 4.2 31.6 1.0
O2 B:CO31002 4.2 11.8 1.0
N B:ALA460 4.3 9.3 1.0
N B:GLU461 4.3 10.1 1.0
CB B:ASP379 4.4 9.0 1.0
ND2 B:ASN432 4.5 8.8 1.0
CG B:GLU461 4.5 8.4 1.0
CA B:GLY381 4.7 7.6 1.0
CA B:ALA460 4.7 10.0 1.0
N B:ASP459 4.8 7.0 1.0
OD2 B:ASP399 4.9 12.1 1.0
CB B:GLU461 5.0 9.8 1.0
NZ B:LYS374 5.0 8.2 1.0
C4 B:BES1003 5.0 35.8 1.0

Magnesium binding site 3 out of 12 in 3kr4

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Magnesium binding site 3 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1004

b:27.1
occ:1.00
OD1 C:ASP459 1.9 11.8 1.0
OD2 C:ASP379 2.1 9.0 1.0
O C:ASP459 2.2 10.3 1.0
O2 C:BES1003 2.2 22.4 1.0
OE1 C:GLU461 2.4 8.1 1.0
O3 C:BES1003 2.6 28.2 1.0
CG C:ASP459 2.9 12.1 1.0
C3 C:BES1003 3.0 27.6 1.0
CG C:ASP379 3.1 10.6 1.0
C2 C:BES1003 3.1 26.8 1.0
C C:ASP459 3.1 11.0 1.0
OD1 C:ASP379 3.3 10.4 1.0
ZN C:ZN1001 3.3 39.1 1.0
CD C:GLU461 3.5 10.2 1.0
NZ C:LYS386 3.5 11.6 1.0
CA C:ASP459 3.5 10.6 1.0
OD2 C:ASP459 3.6 12.2 1.0
C1 C:BES1003 3.7 24.4 1.0
CB C:ASP459 3.7 10.9 1.0
OE2 C:GLU461 3.8 11.6 1.0
CE C:LYS386 3.9 11.9 1.0
N2 C:BES1003 4.0 24.3 1.0
N1 C:BES1003 4.1 30.0 1.0
O1 C:CO31002 4.3 12.9 1.0
N C:ALA460 4.4 9.7 1.0
CB C:ASP379 4.5 8.6 1.0
N C:GLU461 4.5 9.5 1.0
C4 C:BES1003 4.7 33.9 1.0
ND2 C:ASN432 4.8 9.4 1.0
CA C:GLY381 4.8 8.4 1.0
CA C:ALA460 4.8 9.8 1.0
CG C:GLU461 4.9 8.5 1.0
N C:ASP459 4.9 10.1 1.0

Magnesium binding site 4 out of 12 in 3kr4

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Magnesium binding site 4 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg1004

b:28.2
occ:1.00
O2 D:BES1003 2.0 13.3 1.0
OD2 D:ASP379 2.0 9.2 1.0
OD1 D:ASP459 2.0 12.0 1.0
OE1 D:GLU461 2.2 12.2 1.0
O D:ASP459 2.2 9.3 1.0
CG D:ASP379 2.9 10.2 1.0
CG D:ASP459 3.1 11.6 1.0
O3 D:BES1003 3.1 22.8 1.0
OD1 D:ASP379 3.1 9.0 1.0
C2 D:BES1003 3.1 22.8 1.0
ZN D:ZN1001 3.1 34.2 1.0
CD D:GLU461 3.1 13.5 1.0
C D:ASP459 3.1 9.3 1.0
C3 D:BES1003 3.3 23.2 1.0
OE2 D:GLU461 3.3 13.5 1.0
CA D:ASP459 3.5 9.6 1.0
NZ D:LYS386 3.8 12.8 1.0
C1 D:BES1003 3.8 23.3 1.0
CB D:ASP459 3.8 9.7 1.0
OD2 D:ASP459 3.9 12.7 1.0
N2 D:BES1003 4.0 20.8 1.0
CE D:LYS386 4.0 11.9 1.0
O1 D:CO31002 4.1 11.6 1.0
N1 D:BES1003 4.3 24.7 1.0
CB D:ASP379 4.3 8.5 1.0
N D:ALA460 4.4 8.6 1.0
N D:GLU461 4.5 10.0 1.0
ND2 D:ASN432 4.5 8.4 1.0
CG D:GLU461 4.5 11.1 1.0
CA D:GLY381 4.8 7.5 1.0
OD2 D:ASP399 4.8 9.9 1.0
N D:ASP459 4.9 9.2 1.0
CA D:ALA460 4.9 8.2 1.0
NZ D:LYS374 4.9 4.4 1.0
O D:THR458 5.0 10.3 1.0

Magnesium binding site 5 out of 12 in 3kr4

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Magnesium binding site 5 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1004

b:26.4
occ:1.00
OE1 E:GLU461 1.8 10.7 1.0
O E:ASP459 2.1 11.6 1.0
OD1 E:ASP459 2.1 12.2 1.0
OD2 E:ASP379 2.2 10.2 1.0
O2 E:BES1003 2.3 19.8 1.0
CD E:GLU461 2.8 12.2 1.0
C E:ASP459 2.9 11.9 1.0
CG E:ASP379 3.0 10.5 1.0
ZN E:ZN1001 3.1 38.3 1.0
OD1 E:ASP379 3.1 11.7 1.0
OE2 E:GLU461 3.2 11.9 1.0
CG E:ASP459 3.2 12.6 1.0
O3 E:BES1003 3.2 29.2 1.0
CA E:ASP459 3.3 11.6 1.0
C2 E:BES1003 3.5 24.6 1.0
C3 E:BES1003 3.5 27.7 1.0
CB E:ASP459 3.8 11.6 1.0
N E:GLU461 4.0 10.3 1.0
N E:ALA460 4.0 11.1 1.0
NZ E:LYS386 4.0 14.6 1.0
O3 E:CO31002 4.2 17.8 1.0
OD2 E:ASP459 4.2 10.7 1.0
CG E:GLU461 4.2 10.0 1.0
ND2 E:ASN432 4.2 9.4 1.0
C1 E:BES1003 4.3 24.9 1.0
N1 E:BES1003 4.4 29.4 1.0
CB E:ASP379 4.4 9.9 1.0
CA E:ALA460 4.5 11.1 1.0
N2 E:BES1003 4.5 19.6 1.0
CE E:LYS386 4.5 11.6 1.0
N E:ASP459 4.6 11.3 1.0
CB E:GLU461 4.6 10.4 1.0
O E:THR458 4.6 11.1 1.0
CA E:GLY381 4.7 10.7 1.0
C E:ALA460 4.8 11.1 1.0
CA E:GLU461 4.9 10.4 1.0
OD2 E:ASP399 4.9 9.7 1.0
NZ E:LYS374 5.0 10.3 1.0

Magnesium binding site 6 out of 12 in 3kr4

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Magnesium binding site 6 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg1004

b:37.5
occ:1.00
OD1 F:ASP459 1.9 11.5 1.0
OD2 F:ASP379 2.0 13.3 1.0
O2 F:BES1003 2.3 13.3 1.0
OE1 F:GLU461 2.3 12.1 1.0
O F:ASP459 2.3 11.1 1.0
CG F:ASP379 2.8 12.8 1.0
O3 F:BES1003 3.0 27.7 1.0
CG F:ASP459 3.0 13.1 1.0
OD1 F:ASP379 3.0 14.6 1.0
ZN F:ZN1001 3.1 40.9 1.0
C2 F:BES1003 3.2 22.7 1.0
C3 F:BES1003 3.2 28.1 1.0
C F:ASP459 3.2 10.8 1.0
CD F:GLU461 3.2 11.1 1.0
OE2 F:GLU461 3.4 9.6 1.0
CA F:ASP459 3.5 10.0 1.0
NZ F:LYS386 3.7 15.4 1.0
C1 F:BES1003 3.8 22.4 1.0
CB F:ASP459 3.8 10.7 1.0
OD2 F:ASP459 3.9 13.3 1.0
CE F:LYS386 4.0 11.6 1.0
N2 F:BES1003 4.0 19.6 1.0
N1 F:BES1003 4.1 32.0 1.0
CB F:ASP379 4.3 11.1 1.0
O1 F:CO31002 4.3 12.6 1.0
N F:ALA460 4.4 10.2 1.0
N F:GLU461 4.5 8.0 1.0
ND2 F:ASN432 4.6 9.3 1.0
CG F:GLU461 4.6 10.6 1.0
CA F:GLY381 4.7 11.1 1.0
OD2 F:ASP399 4.8 20.6 1.0
C4 F:BES1003 4.9 35.2 1.0
NZ F:LYS374 4.9 5.2 1.0
N F:ASP459 4.9 7.8 1.0
N F:GLY381 4.9 11.1 1.0
CA F:ALA460 5.0 10.1 1.0

Magnesium binding site 7 out of 12 in 3kr4

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Magnesium binding site 7 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Mg1004

b:23.7
occ:1.00
OD2 G:ASP379 2.0 7.0 1.0
OD1 G:ASP459 2.0 11.9 1.0
O2 G:BES1003 2.2 13.8 1.0
OE1 G:GLU461 2.2 8.5 1.0
O G:ASP459 2.4 11.3 1.0
CG G:ASP379 2.8 8.2 1.0
OD1 G:ASP379 3.0 7.9 1.0
O3 G:BES1003 3.0 28.3 1.0
CG G:ASP459 3.0 12.5 1.0
ZN G:ZN1001 3.1 38.2 1.0
CD G:GLU461 3.2 11.0 1.0
C2 G:BES1003 3.2 24.0 1.0
C G:ASP459 3.2 10.3 1.0
C3 G:BES1003 3.3 26.3 1.0
OE2 G:GLU461 3.5 11.1 1.0
CA G:ASP459 3.5 10.2 1.0
NZ G:LYS386 3.6 11.6 1.0
C1 G:BES1003 3.8 22.9 1.0
CB G:ASP459 3.8 10.7 1.0
OD2 G:ASP459 3.9 16.2 1.0
CE G:LYS386 3.9 8.9 1.0
N2 G:BES1003 4.1 15.9 1.0
N1 G:BES1003 4.2 30.1 1.0
CB G:ASP379 4.2 7.4 1.0
O2 G:CO31002 4.4 11.8 1.0
N G:ALA460 4.4 9.1 1.0
ND2 G:ASN432 4.4 7.5 1.0
N G:GLU461 4.5 8.5 1.0
CG G:GLU461 4.6 9.8 1.0
CA G:GLY381 4.7 7.9 1.0
OD2 G:ASP399 4.8 12.9 1.0
N G:ASP459 4.9 9.1 1.0
CA G:ALA460 4.9 9.8 1.0
N G:GLY381 4.9 7.2 1.0
C4 G:BES1003 5.0 32.6 1.0

Magnesium binding site 8 out of 12 in 3kr4

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Magnesium binding site 8 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mg1004

b:40.7
occ:1.00
OD1 H:ASP459 1.8 11.7 1.0
OD2 H:ASP379 2.2 8.3 1.0
O H:ASP459 2.2 10.4 1.0
OE1 H:GLU461 2.3 11.3 1.0
O2 H:BES1003 2.3 16.5 1.0
CG H:ASP459 2.9 11.4 1.0
O3 H:BES1003 3.0 22.7 1.0
CG H:ASP379 3.0 9.3 1.0
C H:ASP459 3.1 9.8 1.0
C3 H:BES1003 3.2 24.5 1.0
ZN H:ZN1001 3.2 34.8 1.0
CD H:GLU461 3.3 10.8 1.0
C2 H:BES1003 3.3 19.6 1.0
OD1 H:ASP379 3.3 6.6 1.0
CA H:ASP459 3.3 8.6 1.0
OE2 H:GLU461 3.5 10.3 1.0
CB H:ASP459 3.7 8.2 1.0
NZ H:LYS386 3.7 9.6 1.0
OD2 H:ASP459 3.8 13.5 1.0
C1 H:BES1003 3.8 19.2 1.0
CE H:LYS386 4.0 7.8 1.0
N1 H:BES1003 4.1 25.2 1.0
N2 H:BES1003 4.1 15.8 1.0
O2 H:CO31002 4.2 10.3 1.0
N H:ALA460 4.3 9.1 1.0
N H:GLU461 4.3 10.4 1.0
CB H:ASP379 4.4 8.8 1.0
ND2 H:ASN432 4.5 8.6 1.0
CG H:GLU461 4.6 8.0 1.0
CA H:GLY381 4.7 7.3 1.0
CA H:ALA460 4.7 9.9 1.0
N H:ASP459 4.7 6.7 1.0
C4 H:BES1003 4.8 30.2 1.0
O H:THR458 5.0 6.5 1.0
OD2 H:ASP399 5.0 11.4 1.0

Magnesium binding site 9 out of 12 in 3kr4

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Magnesium binding site 9 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Mg1004

b:15.1
occ:1.00
OE1 I:GLU461 2.0 8.1 1.0
OD1 I:ASP459 2.0 11.6 1.0
OD2 I:ASP379 2.0 8.2 1.0
O2 I:BES1003 2.2 11.2 1.0
O I:ASP459 2.2 9.6 1.0
CG I:ASP379 2.8 10.2 1.0
CD I:GLU461 2.9 9.5 1.0
OD1 I:ASP379 3.0 10.4 1.0
C I:ASP459 3.1 10.6 1.0
CG I:ASP459 3.1 11.9 1.0
ZN I:ZN1001 3.2 36.9 1.0
OE2 I:GLU461 3.2 11.9 1.0
O3 I:BES1003 3.2 25.1 1.0
C2 I:BES1003 3.4 22.5 1.0
CA I:ASP459 3.5 10.3 1.0
C3 I:BES1003 3.5 24.5 1.0
NZ I:LYS386 3.9 12.1 1.0
CB I:ASP459 3.9 10.7 1.0
OD2 I:ASP459 4.0 11.6 1.0
C1 I:BES1003 4.1 22.6 1.0
CE I:LYS386 4.2 11.4 1.0
N2 I:BES1003 4.2 20.4 1.0
ND2 I:ASN432 4.3 9.7 1.0
N I:GLU461 4.3 9.1 1.0
O1 I:CO31002 4.3 15.7 1.0
N I:ALA460 4.3 9.6 1.0
CB I:ASP379 4.3 8.2 1.0
CG I:GLU461 4.4 8.4 1.0
N1 I:BES1003 4.4 27.2 1.0
CA I:GLY381 4.7 8.0 1.0
CA I:ALA460 4.8 9.4 1.0
CB I:GLU461 4.8 9.0 1.0
OD2 I:ASP399 4.8 10.4 1.0
N I:ASP459 4.9 9.7 1.0
O I:THR458 4.9 8.6 1.0
NZ I:LYS374 4.9 8.1 1.0

Magnesium binding site 10 out of 12 in 3kr4

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Magnesium binding site 10 out of 12 in the Structure of A Protease 3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 10 of Structure of A Protease 3 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mg1004

b:23.0
occ:1.00
OD1 J:ASP459 1.9 11.6 1.0
OD2 J:ASP379 2.0 8.2 1.0
OE2 J:GLU461 2.2 12.9 1.0
O2 J:BES1003 2.2 11.3 1.0
O J:ASP459 2.3 9.7 1.0
CG J:ASP379 2.8 10.2 1.0
OD1 J:ASP379 2.9 8.6 1.0
CG J:ASP459 2.9 11.3 1.0
C J:ASP459 3.1 9.5 1.0
O3 J:BES1003 3.1 28.9 1.0
CD J:GLU461 3.1 13.4 1.0
C2 J:BES1003 3.2 23.9 1.0
ZN J:ZN1001 3.3 38.0 1.0
OE1 J:GLU461 3.3 12.4 1.0
CA J:ASP459 3.3 9.9 1.0
C3 J:BES1003 3.3 26.1 1.0
CB J:ASP459 3.7 10.5 1.0
NZ J:LYS386 3.7 13.5 1.0
OD2 J:ASP459 3.8 12.6 1.0
C1 J:BES1003 3.8 22.4 1.0
CE J:LYS386 4.0 12.4 1.0
N2 J:BES1003 4.2 23.6 1.0
CB J:ASP379 4.3 9.1 1.0
N J:ALA460 4.3 8.3 1.0
O3 J:CO31002 4.3 16.0 1.0
N1 J:BES1003 4.3 30.3 1.0
ND2 J:ASN432 4.4 8.8 1.0
N J:GLU461 4.4 9.5 1.0
CG J:GLU461 4.5 11.0 1.0
CA J:GLY381 4.5 8.8 1.0
N J:ASP459 4.7 9.7 1.0
CA J:ALA460 4.8 8.2 1.0
O J:THR458 4.9 10.1 1.0
N J:GLY381 4.9 8.9 1.0
OD2 J:ASP399 4.9 9.9 1.0
CB J:GLU461 5.0 10.4 1.0

Reference:

S.Mcgowan, C.A.Oellig, W.A.Birru, T.T.Caradoc-Davies, C.M.Stack, J.Lowther, T.Skinner-Adams, A.Mucha, P.Kafarski, J.Grembecka, K.R.Trenholme, A.M.Buckle, D.L.Gardiner, J.P.Dalton, J.C.Whisstock. Structure of the Plasmodium Falciparum M17 Aminopeptidase and Significance For the Design of Drugs Targeting the Neutral Exopeptidases Proc.Natl.Acad.Sci.Usa V. 107 2449 2010.
ISSN: ISSN 0027-8424
PubMed: 20133789
DOI: 10.1073/PNAS.0911813107
Page generated: Mon Dec 14 08:23:04 2020

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