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Calcium in PDB 1k93: Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin

Enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin

All present enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin:
4.6.1.1;

Protein crystallography data

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, PDB code: 1k93 was solved by C.L.Drum, S.-Z.Yan, J.Bard, Y.-Q.Shen, D.Lu, S.Soelaiman, Z.Grabarek, A.Bohm, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.95
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.730, 167.311, 344.296, 90.00, 90.00, 90.00
R / Rfree (%) 27.8 / 31.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin (pdb code 1k93). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin, PDB code: 1k93:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 1 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:57.0
occ:1.00
 OD1 D:ASP133 1.8 82.4 1.0
OE2 D:GLU140 2.4 67.1 1.0
CG D:ASP133 2.5 80.9 1.0
OE1 D:GLU140 2.5 70.5 1.0
O D:GLN135 2.6 71.0 1.0
OD2 D:ASP133 2.6 82.7 1.0
OD1 D:ASP131 2.7 83.6 1.0
CD D:GLU140 2.8 68.4 1.0
OD2 D:ASP129 3.5 83.2 1.0
CG D:ASP131 3.5 82.7 1.0
OD1 D:ASP129 3.5 83.0 1.0
CG D:ASP129 3.5 82.5 1.0
C D:GLN135 3.7 72.6 1.0
OD2 D:ASP131 3.8 83.8 1.0
CB D:ASP133 3.9 79.9 1.0
N D:ASP133 3.9 80.4 1.0
N D:ASP131 4.1 79.8 1.0
N D:ILE130 4.1 80.3 1.0
CG D:GLU140 4.3 67.8 1.0
CA D:ASP129 4.4 82.5 1.0
CB D:ASP129 4.4 82.1 1.0
CA D:VAL136 4.4 72.5 1.0
N D:GLY132 4.4 80.2 1.0
N D:GLN135 4.4 75.5 1.0
CA D:ASP133 4.5 79.8 1.0
N D:VAL136 4.5 72.4 1.0
N D:ASN137 4.7 71.1 1.0
CA D:GLN135 4.7 74.3 1.0
CB D:ASP131 4.7 82.4 1.0
CA D:ASP131 4.7 80.5 1.0
C D:ASP129 4.8 81.5 1.0
C D:ASP131 4.8 80.2 1.0
N D:GLY134 4.8 77.1 1.0
C D:ASP133 5.0 79.2 1.0
ND2 D:ASN137 5.0 69.0 1.0
C D:GLY132 5.0 79.9 1.0

Calcium binding site 2 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 2 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca802

b:62.0
occ:1.00
 OD1 D:ASN97 2.3 73.1 1.0
OE1 D:GLU104 2.4 81.7 1.0
OD1 D:ASP95 2.4 79.2 1.0
O D:TYR99 2.4 71.2 1.0
CD D:GLU104 2.7 83.2 1.0
OE2 D:GLU104 2.7 83.7 1.0
OD1 D:ASP93 2.9 70.4 1.0
CG D:ASN97 3.0 72.8 1.0
ND2 D:ASN97 3.2 73.4 1.0
CG D:ASP95 3.3 76.2 1.0
OD2 D:ASP95 3.5 79.5 1.0
C D:TYR99 3.6 72.1 1.0
CG D:GLU104 3.9 84.0 1.0
CG D:ASP93 4.0 71.6 1.0
N D:SER101 4.1 76.0 1.0
CA D:ILE100 4.3 73.5 1.0
CB D:ASN97 4.4 73.1 1.0
N D:ILE100 4.4 72.5 1.0
CA D:ASP93 4.5 70.8 1.0
OG D:SER101 4.5 76.4 1.0
CA D:TYR99 4.5 72.9 1.0
N D:TYR99 4.5 73.3 1.0
CB D:SER101 4.5 77.3 1.0
C D:ILE100 4.6 73.9 1.0
CB D:ASP95 4.7 75.0 1.0
N D:ASP95 4.7 73.5 1.0
OD2 D:ASP93 4.7 72.8 1.0
CB D:ASP93 4.8 70.5 1.0
N D:ASN97 4.8 72.2 1.0
C D:ASP93 4.8 72.1 1.0
CB D:TYR99 4.9 73.0 1.0
CB D:GLU104 5.0 84.3 1.0
CA D:SER101 5.0 77.6 1.0

Calcium binding site 3 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 3 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca803

b:79.2
occ:1.00
 O E:GLN135 1.8 79.4 1.0
OD1 E:ASP133 2.1 89.3 1.0
OE1 E:GLU140 2.3 76.9 1.0
OD2 E:ASP133 2.4 87.7 1.0
CG E:ASP133 2.6 88.2 1.0
C E:GLN135 2.9 80.8 1.0
CD E:GLU140 2.9 76.1 1.0
OE2 E:GLU140 2.9 73.6 1.0
OD2 E:ASP129 3.5 86.1 1.0
OD1 E:ASP131 3.5 88.0 1.0
CA E:VAL136 3.5 79.0 1.0
N E:VAL136 3.6 80.3 1.0
CG E:ASP129 3.7 86.2 1.0
N E:GLN135 3.9 82.0 1.0
OD1 E:ASP129 3.9 85.2 1.0
CA E:GLN135 4.0 81.5 1.0
N E:ASN137 4.0 76.6 1.0
CB E:ASP133 4.1 86.2 1.0
C E:VAL136 4.2 78.0 1.0
CA E:ASP129 4.3 86.5 1.0
CB E:ASP129 4.4 85.9 1.0
N E:ASP133 4.4 85.8 1.0
CG E:ASP131 4.4 88.6 1.0
CG E:GLU140 4.4 75.1 1.0
N E:ILE130 4.5 84.7 1.0
CG E:GLN135 4.6 82.8 1.0
CB E:GLN135 4.6 81.7 1.0
OD2 E:ASP131 4.6 90.0 1.0
CA E:ASP133 4.7 85.1 1.0
N E:GLY134 4.7 83.6 1.0
CB E:VAL136 4.8 79.4 1.0
N E:ASP131 4.9 85.5 1.0
ND2 E:ASN137 4.9 77.5 1.0
C E:ASP133 4.9 84.2 1.0
CG2 E:VAL136 5.0 78.9 1.0
C E:ASP129 5.0 85.9 1.0

Calcium binding site 4 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 4 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca804

b:82.0
occ:1.00
 OD1 E:ASP95 2.1 81.5 1.0
OD1 E:ASN97 2.2 78.5 1.0
OE1 E:GLU104 2.5 83.9 1.0
O E:TYR99 2.6 75.7 1.0
OE2 E:GLU104 2.6 82.3 1.0
CD E:GLU104 2.7 83.3 1.0
OD1 E:ASP93 2.8 72.0 1.0
CG E:ASN97 2.9 78.6 1.0
CG E:ASP95 3.0 79.9 1.0
OD2 E:ASP95 3.1 79.9 1.0
ND2 E:ASN97 3.2 80.3 1.0
C E:TYR99 3.8 77.8 1.0
CG E:ASP93 3.9 71.6 1.0
CG E:GLU104 4.0 84.5 1.0
CB E:ASN97 4.1 77.4 1.0
CB E:ASP95 4.3 78.3 1.0
N E:ASP95 4.4 77.3 1.0
N E:SER101 4.5 81.7 1.0
CA E:ASP93 4.5 71.3 1.0
N E:ASN97 4.5 77.4 1.0
N E:TYR99 4.6 77.1 1.0
CA E:ILE100 4.6 79.6 1.0
N E:ILE100 4.6 78.5 1.0
CA E:TYR99 4.7 77.6 1.0
OD2 E:ASP93 4.7 71.3 1.0
C E:ASP93 4.7 72.0 1.0
CB E:ASP93 4.7 71.0 1.0
CB E:SER101 4.8 82.5 1.0
N E:GLY96 4.8 75.0 1.0
OG E:SER101 4.8 81.8 1.0
CA E:ASP95 4.9 77.1 1.0
N E:LYS94 4.9 73.9 1.0
CA E:ASN97 4.9 77.7 1.0
C E:ILE100 5.0 81.2 1.0

Calcium binding site 5 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 5 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca805

b:66.7
occ:1.00
 OD1 F:ASP133 2.1 86.0 1.0
OE2 F:GLU140 2.2 68.1 1.0
OE1 F:GLU140 2.2 69.8 1.0
CD F:GLU140 2.4 68.4 1.0
O F:GLN135 2.7 76.4 1.0
CG F:ASP133 2.7 86.3 1.0
OD2 F:ASP133 2.8 87.3 1.0
OD1 F:ASP131 2.8 85.5 1.0
CG F:ASP131 3.5 85.5 1.0
OD1 F:ASP129 3.6 82.7 1.0
CG F:ASP129 3.7 83.2 1.0
OD2 F:ASP131 3.7 85.4 1.0
OD2 F:ASP129 3.7 82.8 1.0
C F:GLN135 3.8 77.6 1.0
CG F:GLU140 3.9 69.4 1.0
N F:ILE130 4.0 81.6 1.0
N F:ASP131 4.1 82.3 1.0
CB F:ASP133 4.1 85.5 1.0
N F:ASP133 4.3 84.6 1.0
CA F:VAL136 4.3 75.8 1.0
CA F:ASP129 4.3 83.8 1.0
N F:ASN137 4.4 74.1 1.0
CB F:ASP129 4.5 83.4 1.0
N F:VAL136 4.5 76.5 1.0
C F:ASP129 4.7 83.1 1.0
ND2 F:ASN137 4.7 73.2 1.0
N F:GLY132 4.7 82.7 1.0
N F:GLN135 4.7 80.4 1.0
CB F:ASP131 4.7 84.7 1.0
CB F:GLU140 4.8 69.0 1.0
CA F:ASP131 4.8 83.0 1.0
CA F:ASP133 4.8 84.5 1.0
C F:VAL136 4.9 75.2 1.0
CA F:GLN135 4.9 78.8 1.0
CA F:ILE130 5.0 80.6 1.0
C F:ASP131 5.0 82.3 1.0

Calcium binding site 6 out of 6 in 1k93

Go back to Calcium Binding Sites List in 1k93
Calcium binding site 6 out of 6 in the Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin


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 the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca806

b:79.1
occ:1.00
 OD1 F:ASN97 2.1 77.3 1.0
O F:TYR99 2.2 75.3 1.0
OD1 F:ASP95 2.5 84.7 1.0
OE1 F:GLU104 2.5 88.7 1.0
OD1 F:ASP93 2.7 69.5 1.0
CG F:ASN97 2.8 78.3 1.0
CD F:GLU104 2.9 88.1 1.0
OE2 F:GLU104 2.9 87.2 1.0
ND2 F:ASN97 3.0 78.8 1.0
C F:TYR99 3.3 76.2 1.0
CG F:ASP95 3.4 81.5 1.0
OD2 F:ASP95 3.5 80.8 1.0
CG F:ASP93 3.7 70.7 1.0
CB F:ASN97 4.2 77.7 1.0
CG F:GLU104 4.2 88.5 1.0
N F:SER101 4.2 79.7 1.0
N F:TYR99 4.2 76.2 1.0
N F:ILE100 4.2 76.4 1.0
CA F:TYR99 4.3 76.3 1.0
CA F:ILE100 4.3 77.2 1.0
CA F:ASP93 4.4 73.4 1.0
OD2 F:ASP93 4.5 69.3 1.0
N F:ASN97 4.5 76.6 1.0
CB F:ASP93 4.6 71.8 1.0
C F:ILE100 4.6 78.5 1.0
CB F:TYR99 4.6 76.6 1.0
CB F:SER101 4.7 80.6 1.0
N F:ASP95 4.8 77.7 1.0
CB F:ASP95 4.8 78.9 1.0
C F:ASP93 4.8 75.7 1.0
OG F:SER101 4.9 79.7 1.0
CA F:ASN97 4.9 76.5 1.0

Reference:

C.L.Drum, S.-Z.Yan, J.Bard, Y.-Q.Shen, D.Lu, S.Soelaiman, Z.Grabarek, A.Bohm, W.-J.Tang. Structural Basis For the Activation of Anthrax Adenylyl Cyclase Exotoxin By Calmodulin. Nature V. 415 396 2002.
ISSN: ISSN 0028-0836
PubMed: 11807546
DOI: 10.1038/415396A
Page generated: Thu Jul 11 11:11:20 2024

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