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:
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
Go back to
Magnesium Binding Sites List in 1xfu
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
Go back to
Magnesium Binding Sites List in 1xfu
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
Go back to
Magnesium Binding Sites List in 1xfu
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
Go back to
Magnesium Binding Sites List in 1xfu
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
Go back to
Magnesium Binding Sites List in 1xfu
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
Go back to
Magnesium Binding Sites List in 1xfu
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
|