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Magnesium in PDB 1xfu: Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin

Enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin

All present enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin, PDB code: 1xfu was solved by Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florian, W.J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 3.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 317.562, 183.108, 141.117, 90.00, 90.05, 90.00
R / Rfree (%) 28.3 / 30

Other elements in 1xfu:

The structure of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin also contains other interesting chemical elements:

Calcium (Ca) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin (pdb code 1xfu). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin, PDB code: 1xfu:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 1xfu

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Magnesium binding site 1 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg900

b:18.9
occ:1.00
 NE2 A:HIS577 2.5 43.5 1.0
OD2 A:ASP491 2.6 52.5 1.0
OD2 A:ASP493 2.6 45.4 1.0
OD1 A:ASP491 2.8 51.7 1.0
CG A:ASP491 3.0 52.3 1.0
OD1 A:ASP493 3.2 44.5 1.0
CG A:ASP493 3.3 44.1 1.0
CE1 A:HIS577 3.4 45.6 1.0
CD2 A:HIS577 3.5 43.9 1.0
O A:LYS346 3.8 46.6 1.0
O A:GLY347 4.1 54.0 1.0
CB A:ASP491 4.5 51.6 1.0
ND1 A:HIS577 4.5 44.4 1.0
CG A:HIS577 4.6 43.4 1.0
CG A:LYS346 4.7 49.8 1.0
C A:LYS346 4.8 47.3 1.0
CB A:ASP493 4.8 42.2 1.0
C A:GLY347 4.9 53.6 1.0

Magnesium binding site 2 out of 6 in 1xfu

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Magnesium binding site 2 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:13.7
occ:1.00
 NE2 B:HIS577 2.4 41.3 1.0
OD2 B:ASP493 2.5 46.8 1.0
OD2 B:ASP491 2.6 52.1 1.0
OD1 B:ASP491 2.7 51.5 1.0
CG B:ASP491 3.0 51.7 1.0
OD1 B:ASP493 3.1 44.4 1.0
CG B:ASP493 3.2 45.2 1.0
CE1 B:HIS577 3.3 43.7 1.0
CD2 B:HIS577 3.4 42.1 1.0
O B:LYS346 3.8 47.4 1.0
O B:GLY347 4.2 53.0 1.0
ND1 B:HIS577 4.4 42.8 1.0
CB B:ASP491 4.5 51.1 1.0
CG B:HIS577 4.5 41.9 1.0
CB B:ASP493 4.6 43.6 1.0
C B:LYS346 4.8 47.4 1.0
CG B:LYS346 4.9 50.0 1.0
C B:GLY347 5.0 52.8 1.0

Magnesium binding site 3 out of 6 in 1xfu

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Magnesium binding site 3 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg902

b:15.0
occ:1.00
 NE2 C:HIS577 2.4 42.7 1.0
OD2 C:ASP493 2.5 44.3 1.0
OD2 C:ASP491 2.6 55.9 1.0
OD1 C:ASP491 2.8 54.7 1.0
CG C:ASP491 3.0 55.0 1.0
OD1 C:ASP493 3.1 42.5 1.0
CG C:ASP493 3.2 43.8 1.0
CE1 C:HIS577 3.3 44.3 1.0
CD2 C:HIS577 3.5 43.3 1.0
O C:LYS346 3.8 47.4 1.0
O C:GLY347 4.2 54.3 1.0
ND1 C:HIS577 4.5 43.4 1.0
CB C:ASP491 4.5 52.9 1.0
CG C:HIS577 4.6 42.7 1.0
CB C:ASP493 4.7 43.0 1.0
CG C:LYS346 4.8 51.8 1.0
C C:LYS346 4.8 48.6 1.0
C C:GLY347 5.0 54.4 1.0

Magnesium binding site 4 out of 6 in 1xfu

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Magnesium binding site 4 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg903

b:19.4
occ:1.00
 OD2 D:ASP491 2.5 54.4 1.0
OD2 D:ASP493 2.6 43.9 1.0
NE2 D:HIS577 2.6 43.6 1.0
OD1 D:ASP491 2.8 53.4 1.0
CG D:ASP491 3.0 53.9 1.0
OD1 D:ASP493 3.1 43.0 1.0
CG D:ASP493 3.2 43.3 1.0
CE1 D:HIS577 3.5 44.9 1.0
CD2 D:HIS577 3.6 43.6 1.0
O D:LYS346 3.7 48.1 1.0
O D:GLY347 4.1 54.6 1.0
CB D:ASP491 4.4 52.5 1.0
ND1 D:HIS577 4.6 43.5 1.0
CG D:LYS346 4.7 50.7 1.0
CB D:ASP493 4.7 42.1 1.0
CG D:HIS577 4.7 43.6 1.0
C D:LYS346 4.8 48.7 1.0
C D:GLY347 5.0 54.1 1.0

Magnesium binding site 5 out of 6 in 1xfu

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Magnesium binding site 5 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg904

b:14.2
occ:1.00
 NE2 E:HIS577 2.4 42.2 1.0
OD2 E:ASP493 2.5 47.0 1.0
OD2 E:ASP491 2.5 52.8 1.0
OD1 E:ASP491 2.7 51.6 1.0
CG E:ASP491 2.9 52.3 1.0
OD1 E:ASP493 3.2 46.6 1.0
CG E:ASP493 3.2 46.4 1.0
CE1 E:HIS577 3.3 43.9 1.0
CD2 E:HIS577 3.4 43.0 1.0
O E:LYS346 3.8 46.6 1.0
O E:GLY347 4.2 52.3 1.0
CB E:ASP491 4.4 51.0 1.0
ND1 E:HIS577 4.5 43.5 1.0
CG E:HIS577 4.6 42.8 1.0
CB E:ASP493 4.7 44.0 1.0
C E:LYS346 4.8 47.1 1.0
CG E:LYS346 4.8 49.7 1.0
C E:GLY347 4.9 52.9 1.0

Magnesium binding site 6 out of 6 in 1xfu

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Magnesium binding site 6 out of 6 in the Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of Anthrax Edema Factor (Ef) Truncation Mutant, Ef- Delta 64 in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg905

b:16.6
occ:1.00
 NE2 F:HIS577 2.4 43.1 1.0
OD2 F:ASP493 2.5 45.7 1.0
OD2 F:ASP491 2.6 54.3 1.0
OD1 F:ASP491 2.8 53.5 1.0
CG F:ASP491 3.0 53.9 1.0
OD1 F:ASP493 3.1 45.3 1.0
CG F:ASP493 3.2 45.2 1.0
CE1 F:HIS577 3.3 44.6 1.0
CD2 F:HIS577 3.5 43.8 1.0
O F:LYS346 3.9 47.2 1.0
O F:GLY347 4.2 53.2 1.0
ND1 F:HIS577 4.5 44.0 1.0
CB F:ASP491 4.5 52.2 1.0
CG F:HIS577 4.6 43.5 1.0
CB F:ASP493 4.6 43.5 1.0
CG F:LYS346 4.9 49.6 1.0
C F:LYS346 4.9 47.6 1.0
C F:GLY347 5.0 53.4 1.0

Reference:

Y.Shen, N.L.Zhukovskaya, Q.Guo, J.Florian, W.J.Tang. Calcium-Independent Calmodulin Binding and Two-Metal-Ion Catalytic Mechanism of Anthrax Edema Factor. Embo J. V. 24 929 2005.
ISSN: ISSN 0261-4189
PubMed: 15719022
DOI: 10.1038/SJ.EMBOJ.7600574
Page generated: Tue Aug 13 17:34:28 2024

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