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Calcium in PDB 1y0v: Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate

Enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate

All present enzymatic activity of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate, PDB code: 1y0v 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) 29.87 / 3.60
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 317.509, 183.348, 141.812, 90.00, 90.05, 90.00
R / Rfree (%) 28.6 / 30.7

Other elements in 1y0v:

The structure of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate (pdb code 1y0v). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 18 binding sites of Calcium where determined in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate, PDB code: 1y0v:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 1 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca701

b:77.4
occ:1.00
 O H:THR26 2.2 77.7 1.0
OD1 H:ASP24 2.5 83.2 1.0
OD1 H:ASP22 2.9 84.2 1.0
OD2 H:ASP22 3.0 84.2 1.0
OD2 H:ASP20 3.0 72.5 1.0
OD2 H:ASP24 3.1 83.7 1.0
CG H:ASP24 3.1 82.5 1.0
CG H:ASP22 3.2 83.6 1.0
C H:THR26 3.4 78.1 1.0
OG1 H:THR26 3.6 80.4 1.0
CG H:ASP20 4.0 72.2 1.0
N H:THR26 4.1 77.7 1.0
OD1 H:ASP20 4.2 72.3 1.0
N H:ILE27 4.2 78.1 1.0
CA H:THR26 4.3 78.5 1.0
CA H:ILE27 4.3 78.2 1.0
O H:ASP22 4.3 79.4 1.0
N H:ASP24 4.5 79.7 1.0
CB H:ASP24 4.5 80.3 1.0
CB H:THR26 4.5 79.6 1.0
CB H:ASP22 4.5 82.2 1.0
C H:ASP22 4.6 80.8 1.0
OE2 H:GLU31 4.7 83.0 1.0
N H:GLY25 4.8 77.3 1.0
CA H:ASP22 5.0 82.2 1.0

Calcium binding site 2 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 2 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca801

b:29.9
occ:1.00
 OD1 H:ASP133 2.0 64.5 1.0
O H:GLN135 2.0 51.4 1.0
OE1 H:GLU140 2.2 54.5 1.0
OD2 H:ASP129 2.2 52.2 1.0
OD1 H:ASP131 2.5 55.2 1.0
CG H:ASP133 2.9 63.3 1.0
CG H:ASP129 3.1 52.8 1.0
CD H:GLU140 3.2 53.4 1.0
C H:GLN135 3.3 51.3 1.0
OD2 H:ASP133 3.3 63.6 1.0
CG H:ASP131 3.4 54.4 1.0
OD1 H:ASP129 3.4 52.7 1.0
OD2 H:ASP131 3.5 53.6 1.0
OE2 H:GLU140 3.8 54.7 1.0
N H:VAL136 4.1 50.1 1.0
CA H:VAL136 4.1 49.2 1.0
ND2 H:ASN137 4.2 57.6 1.0
CB H:ASP133 4.2 62.6 1.0
N H:GLN135 4.2 55.9 1.0
CB H:ASP129 4.3 53.7 1.0
N H:ASP133 4.3 59.6 1.0
CA H:GLN135 4.3 52.5 1.0
N H:ASN137 4.3 53.5 1.0
CG H:GLU140 4.4 51.3 1.0
CA H:ASP129 4.5 54.6 1.0
CA H:ASP133 4.6 60.5 1.0
C H:VAL136 4.7 51.8 1.0
N H:ASP131 4.7 52.7 1.0
C H:ASP133 4.7 60.4 1.0
CB H:ASP131 4.7 53.8 1.0
N H:ILE130 4.8 54.8 1.0
CG H:ASN137 4.9 57.1 1.0

Calcium binding site 3 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 3 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca802

b:51.3
occ:1.00
 OD1 H:ASP95 1.9 62.9 1.0
OE1 H:GLU104 2.1 47.4 1.0
ND2 H:ASN97 2.1 60.7 1.0
O H:TYR99 2.2 46.8 1.0
OD1 H:ASN97 2.4 60.5 1.0
CG H:ASN97 2.5 60.9 1.0
CD H:GLU104 2.7 48.2 1.0
OE2 H:GLU104 2.8 48.8 1.0
OD1 H:ASP93 3.0 49.5 1.0
CG H:ASP95 3.0 62.9 1.0
OD2 H:ASP95 3.4 63.8 1.0
C H:TYR99 3.4 46.4 1.0
CG H:ASP93 3.9 49.6 1.0
CA H:ASP93 4.0 48.7 1.0
CB H:ASN97 4.0 60.7 1.0
CA H:ILE100 4.1 48.5 1.0
OG H:SER101 4.1 48.3 1.0
N H:ASP95 4.2 62.8 1.0
CG H:GLU104 4.2 48.2 1.0
N H:ILE100 4.2 47.2 1.0
N H:LYS94 4.3 57.1 1.0
C H:ASP93 4.3 53.0 1.0
CB H:ASP95 4.3 63.1 1.0
N H:TYR99 4.3 49.1 1.0
N H:ASN97 4.4 62.9 1.0
CA H:TYR99 4.4 46.5 1.0
CB H:ASP93 4.5 49.0 1.0
C H:ILE100 4.5 50.6 1.0
CA H:ASN97 4.7 60.5 1.0
OD2 H:ASP93 4.7 49.8 1.0
CA H:ASP95 4.8 63.0 1.0
N H:SER101 4.8 50.8 1.0
N H:GLY96 4.8 62.4 1.0
CB H:TYR99 4.9 45.7 1.0
O H:ILE100 4.9 53.1 1.0
C H:ASN97 5.0 58.8 1.0
O H:ASP93 5.0 54.1 1.0
N H:GLY98 5.0 57.4 1.0

Calcium binding site 4 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 4 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca703

b:73.2
occ:1.00
 O I:THR26 2.4 77.6 1.0
OD1 I:ASP24 2.5 83.9 1.0
OD2 I:ASP22 2.8 85.3 1.0
OD1 I:ASP22 2.9 85.2 1.0
OD2 I:ASP24 3.0 84.2 1.0
CG I:ASP24 3.0 82.9 1.0
CG I:ASP22 3.1 84.2 1.0
OD2 I:ASP20 3.1 69.2 1.0
C I:THR26 3.5 77.7 1.0
OG1 I:THR26 3.6 80.1 1.0
CG I:ASP20 4.1 69.6 1.0
O I:ASP22 4.2 79.9 1.0
N I:THR26 4.3 78.6 1.0
OD1 I:ASP20 4.3 68.4 1.0
CA I:THR26 4.4 78.3 1.0
N I:ILE27 4.4 77.6 1.0
CB I:ASP22 4.4 82.6 1.0
N I:ASP24 4.4 80.2 1.0
CA I:ILE27 4.4 77.6 1.0
CB I:ASP24 4.4 80.8 1.0
C I:ASP22 4.6 81.5 1.0
CB I:THR26 4.6 79.2 1.0
N I:GLY25 4.8 77.7 1.0
OE2 I:GLU31 4.9 83.4 1.0
CA I:ASP22 4.9 82.8 1.0
CA I:ASP24 5.0 80.0 1.0

Calcium binding site 5 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 5 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca803

b:24.6
occ:1.00
 OD1 I:ASP133 2.0 65.2 1.0
O I:GLN135 2.1 50.6 1.0
OE1 I:GLU140 2.1 54.2 1.0
OD2 I:ASP129 2.2 49.6 1.0
OD1 I:ASP131 2.5 56.6 1.0
CG I:ASP133 3.0 63.4 1.0
CG I:ASP129 3.1 50.8 1.0
CD I:GLU140 3.2 53.2 1.0
C I:GLN135 3.3 50.9 1.0
CG I:ASP131 3.3 55.7 1.0
OD2 I:ASP133 3.4 63.6 1.0
OD1 I:ASP129 3.4 50.8 1.0
OD2 I:ASP131 3.5 55.5 1.0
OE2 I:GLU140 3.7 54.3 1.0
CA I:VAL136 4.1 49.1 1.0
N I:VAL136 4.1 50.3 1.0
ND2 I:ASN137 4.2 56.6 1.0
CB I:ASP129 4.3 52.7 1.0
CB I:ASP133 4.3 62.6 1.0
N I:GLN135 4.3 55.6 1.0
N I:ASP133 4.3 60.0 1.0
CA I:GLN135 4.3 52.2 1.0
N I:ASN137 4.3 53.2 1.0
CG I:GLU140 4.4 51.0 1.0
CA I:ASP129 4.5 54.4 1.0
CA I:ASP133 4.6 61.0 1.0
N I:ASP131 4.6 53.1 1.0
C I:VAL136 4.7 50.9 1.0
CB I:ASP131 4.7 54.6 1.0
C I:ASP133 4.7 61.2 1.0
N I:ILE130 4.7 54.9 1.0
CG I:ASN137 4.9 56.1 1.0

Calcium binding site 6 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 6 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca804

b:50.2
occ:1.00
 OD1 I:ASP95 1.9 64.0 1.0
ND2 I:ASN97 2.0 59.3 1.0
OE1 I:GLU104 2.1 50.6 1.0
O I:TYR99 2.2 45.9 1.0
OD1 I:ASN97 2.3 60.1 1.0
CG I:ASN97 2.5 59.9 1.0
CD I:GLU104 2.8 51.0 1.0
OE2 I:GLU104 2.9 51.3 1.0
OD1 I:ASP93 2.9 50.9 1.0
CG I:ASP95 3.0 63.7 1.0
OD2 I:ASP95 3.4 64.3 1.0
C I:TYR99 3.4 45.5 1.0
CG I:ASP93 3.8 50.6 1.0
CB I:ASN97 3.9 59.5 1.0
CA I:ASP93 4.0 48.8 1.0
CA I:ILE100 4.2 47.3 1.0
N I:ASP95 4.2 62.2 1.0
OG I:SER101 4.2 46.3 1.0
N I:TYR99 4.2 47.8 1.0
N I:ILE100 4.2 46.0 1.0
CG I:GLU104 4.3 50.5 1.0
N I:LYS94 4.3 57.6 1.0
CB I:ASP95 4.3 63.8 1.0
C I:ASP93 4.3 53.1 1.0
N I:ASN97 4.3 61.7 1.0
CA I:TYR99 4.4 45.6 1.0
CB I:ASP93 4.5 49.7 1.0
C I:ILE100 4.5 49.0 1.0
CA I:ASN97 4.6 59.4 1.0
OD2 I:ASP93 4.7 50.9 1.0
CA I:ASP95 4.8 62.8 1.0
N I:GLY96 4.8 61.6 1.0
CB I:TYR99 4.9 44.8 1.0
C I:ASN97 4.9 57.9 1.0
N I:GLY98 4.9 56.6 1.0
N I:SER101 4.9 49.6 1.0
O I:ILE100 5.0 52.0 1.0
O I:ASP93 5.0 53.8 1.0

Calcium binding site 7 out of 18 in 1y0v

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Calcium binding site 7 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca705

b:72.4
occ:1.00
 O J:THR26 2.4 77.8 1.0
OD1 J:ASP24 2.7 82.6 1.0
OD2 J:ASP22 2.8 84.5 1.0
OD1 J:ASP22 2.8 84.2 1.0
OD2 J:ASP24 3.1 83.1 1.0
CG J:ASP22 3.1 83.9 1.0
OD2 J:ASP20 3.1 70.8 1.0
CG J:ASP24 3.2 81.8 1.0
C J:THR26 3.5 78.3 1.0
OG1 J:THR26 3.6 80.5 1.0
CG J:ASP20 4.1 71.1 1.0
O J:ASP22 4.3 80.2 1.0
N J:THR26 4.3 78.6 1.0
N J:ILE27 4.4 77.9 1.0
CA J:ILE27 4.4 77.7 1.0
OD1 J:ASP20 4.4 70.7 1.0
CA J:THR26 4.4 78.8 1.0
CB J:ASP22 4.4 82.6 1.0
N J:ASP24 4.6 79.0 1.0
CB J:ASP24 4.6 80.2 1.0
CB J:THR26 4.6 80.0 1.0
C J:ASP22 4.6 81.3 1.0
OE2 J:GLU31 4.7 82.3 1.0
N J:GLY25 4.9 77.4 1.0
CA J:ASP22 4.9 82.7 1.0

Calcium binding site 8 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 8 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca805

b:28.2
occ:1.00
 OD1 J:ASP133 2.0 64.0 1.0
O J:GLN135 2.1 52.2 1.0
OE1 J:GLU140 2.1 52.9 1.0
OD2 J:ASP129 2.2 49.9 1.0
OD1 J:ASP131 2.4 57.5 1.0
CG J:ASP133 2.9 62.6 1.0
CG J:ASP129 3.1 51.1 1.0
CD J:GLU140 3.2 52.2 1.0
CG J:ASP131 3.3 56.2 1.0
C J:GLN135 3.3 52.2 1.0
OD2 J:ASP133 3.4 62.7 1.0
OD2 J:ASP131 3.5 55.6 1.0
OD1 J:ASP129 3.5 51.3 1.0
OE2 J:GLU140 3.7 53.5 1.0
CA J:VAL136 4.1 50.0 1.0
N J:VAL136 4.1 51.2 1.0
ND2 J:ASN137 4.2 56.3 1.0
CB J:ASP133 4.2 61.9 1.0
CB J:ASP129 4.3 52.6 1.0
N J:ASP133 4.3 59.7 1.0
N J:GLN135 4.3 56.7 1.0
N J:ASN137 4.3 54.0 1.0
CA J:GLN135 4.4 53.6 1.0
CG J:GLU140 4.4 50.5 1.0
CA J:ASP129 4.6 54.5 1.0
CA J:ASP133 4.6 60.8 1.0
N J:ASP131 4.6 53.8 1.0
C J:VAL136 4.7 51.9 1.0
CB J:ASP131 4.7 54.6 1.0
N J:ILE130 4.7 54.5 1.0
C J:ASP133 4.7 61.0 1.0
CG J:ASN137 4.9 56.4 1.0

Calcium binding site 9 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 9 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca806

b:44.6
occ:1.00
 OD1 J:ASP95 2.0 63.6 1.0
ND2 J:ASN97 2.0 61.5 1.0
OE1 J:GLU104 2.1 48.5 1.0
O J:TYR99 2.2 46.8 1.0
OD1 J:ASN97 2.4 61.1 1.0
CG J:ASN97 2.5 61.6 1.0
CD J:GLU104 2.7 49.5 1.0
OE2 J:GLU104 2.8 50.0 1.0
OD1 J:ASP93 3.0 50.6 1.0
CG J:ASP95 3.0 63.3 1.0
OD2 J:ASP95 3.4 64.2 1.0
C J:TYR99 3.4 46.3 1.0
CG J:ASP93 3.9 50.5 1.0
CB J:ASN97 4.0 61.2 1.0
CA J:ASP93 4.0 48.6 1.0
OG J:SER101 4.1 46.7 1.0
CA J:ILE100 4.1 47.6 1.0
CG J:GLU104 4.2 49.8 1.0
N J:ASP95 4.2 62.1 1.0
N J:ILE100 4.2 46.5 1.0
N J:TYR99 4.3 48.2 1.0
N J:LYS94 4.3 56.8 1.0
CB J:ASP95 4.3 63.2 1.0
C J:ASP93 4.3 52.6 1.0
N J:ASN97 4.4 63.3 1.0
CA J:TYR99 4.4 46.1 1.0
C J:ILE100 4.5 50.0 1.0
CB J:ASP93 4.5 49.7 1.0
CA J:ASN97 4.7 60.9 1.0
OD2 J:ASP93 4.7 51.0 1.0
CA J:ASP95 4.8 63.0 1.0
N J:SER101 4.8 50.4 1.0
N J:GLY96 4.9 62.3 1.0
CB J:TYR99 4.9 45.4 1.0
O J:ILE100 4.9 52.5 1.0
C J:ASN97 5.0 58.7 1.0
N J:GLY98 5.0 56.3 1.0

Calcium binding site 10 out of 18 in 1y0v

Go back to Calcium Binding Sites List in 1y0v
Calcium binding site 10 out of 18 in the Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Anthrax Edema Factor (Ef) in Complex with Calmodulin and Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca707

b:74.0
occ:1.00
 O K:THR26 2.5 77.8 1.0
OD1 K:ASP24 2.6 83.4 1.0
OD1 K:ASP22 2.7 83.4 1.0
OD2 K:ASP22 2.7 83.7 1.0
CG K:ASP22 2.9 83.2 1.0
OD2 K:ASP20 3.0 68.8 1.0
OD2 K:ASP24 3.1 82.8 1.0
CG K:ASP24 3.1 82.2 1.0
C K:THR26 3.6 77.9 1.0
OG1 K:THR26 3.8 80.8 1.0
CG K:ASP20 4.0 69.6 1.0
O K:ASP22 4.1 80.0 1.0
OD1 K:ASP20 4.3 69.0 1.0
CB K:ASP22 4.3 82.5 1.0
N K:THR26 4.4 78.5 1.0
N K:ASP24 4.4 79.6 1.0
C K:ASP22 4.4 81.4 1.0
CA K:ILE27 4.5 77.5 1.0
N K:ILE27 4.5 77.6 1.0
CA K:THR26 4.5 78.7 1.0
CB K:ASP24 4.5 80.2 1.0
CA K:ASP22 4.8 82.7 1.0
OE2 K:GLU31 4.8 82.9 1.0
CB K:THR26 4.8 79.9 1.0
N K:ASP22 4.8 82.4 1.0
N K:GLY25 4.9 76.5 1.0

Reference:

Y.Shen, N.L.Zhukovskaya, Q.Guo, 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: Fri Jul 12 07:49:50 2024

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