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Calcium in PDB 1k90: Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

Enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp

All present enzymatic activity of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp:
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 and 3' Deoxy-Atp, PDB code: 1k90 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) 19.97 / 2.75
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 116.099, 166.100, 343.330, 90.00, 90.00, 90.00
R / Rfree (%) 21.5 / 28.6

Other elements in 1k90:

The structure of Crystal Structure of the Adenylyl Cyclase Domain of Anthrax Edema Factor (Ef) in Complex with Calmodulin and 3' Deoxy-Atp also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms

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 and 3' Deoxy-Atp (pdb code 1k90). 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 and 3' Deoxy-Atp, PDB code: 1k90:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1k90

Go back to Calcium Binding Sites List in 1k90
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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca800

b:53.8
occ:1.00
 OD1 D:ASP133 2.1 66.4 1.0
OE2 D:GLU140 2.2 44.6 1.0
O D:GLN135 2.3 67.3 1.0
OD1 D:ASP131 2.3 74.0 1.0
OE1 D:GLU140 2.4 62.3 1.0
CD D:GLU140 2.6 64.7 1.0
OD2 D:ASP129 2.6 88.1 1.0
CG D:ASP131 3.0 53.6 1.0
OD2 D:ASP131 3.1 81.4 1.0
CG D:ASP133 3.2 65.8 1.0
CG D:ASP129 3.3 31.8 1.0
C D:GLN135 3.5 74.2 1.0
OD1 D:ASP129 3.8 38.6 1.0
OD2 D:ASP133 3.8 64.7 1.0
CG D:GLU140 4.1 71.0 1.0
N D:ASP131 4.1 43.8 1.0
CB D:ASP129 4.2 30.6 1.0
N D:ILE130 4.2 69.6 1.0
N D:ASP133 4.3 39.7 1.0
CA D:ASP129 4.3 59.5 1.0
CB D:ASP131 4.3 52.8 1.0
CA D:VAL136 4.4 62.9 1.0
N D:GLN135 4.4 78.5 1.0
CB D:ASP133 4.4 83.8 1.0
N D:VAL136 4.4 65.3 1.0
N D:GLY132 4.5 79.9 1.0
CA D:GLN135 4.5 68.6 1.0
CA D:ASP131 4.6 59.4 1.0
C D:ASP129 4.7 52.8 1.0
C D:ASP131 4.8 46.9 1.0
N D:ASN137 4.8 51.3 1.0
CA D:ASP133 4.8 44.6 1.0
ND2 D:ASN137 4.9 46.4 1.0
N D:GLY134 5.0 25.6 1.0

Calcium binding site 2 out of 6 in 1k90

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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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:59.2
occ:1.00
 OD1 D:ASN97 2.1 46.7 1.0
O D:TYR99 2.1 41.3 1.0
OE2 D:GLU104 2.2 60.4 1.0
OD1 D:ASP95 2.4 41.7 1.0
OE1 D:GLU104 2.6 51.8 1.0
CD D:GLU104 2.7 77.9 1.0
OD2 D:ASP93 3.0 73.8 1.0
CG D:ASN97 3.1 67.8 1.0
C D:TYR99 3.3 42.9 1.0
CG D:ASP95 3.5 55.5 1.0
CG D:ASP93 3.6 45.8 1.0
ND2 D:ASN97 3.6 70.7 1.0
OD2 D:ASP95 4.1 0.4 1.0
CG D:GLU104 4.1 0.8 1.0
CA D:ASP93 4.1 50.0 1.0
CB D:ASP93 4.1 57.5 1.0
N D:TYR99 4.2 84.9 1.0
N D:ILE100 4.2 40.4 1.0
N D:SER101 4.2 83.9 1.0
CA D:TYR99 4.2 69.8 1.0
CA D:ILE100 4.2 63.0 1.0
OD1 D:ASP93 4.3 72.3 1.0
CB D:ASN97 4.4 71.5 1.0
N D:ASN97 4.4 28.7 1.0
OG D:SER101 4.5 50.2 1.0
C D:ILE100 4.6 69.0 1.0
CB D:TYR99 4.6 42.1 1.0
C D:ASP93 4.7 40.2 1.0
CB D:SER101 4.7 42.7 1.0
CB D:ASP95 4.7 48.2 1.0
N D:ASP95 4.8 28.3 1.0
N D:GLY96 4.8 40.8 1.0
CA D:ASN97 4.9 65.1 1.0
N D:LYS94 4.9 65.1 1.0

Calcium binding site 3 out of 6 in 1k90

Go back to Calcium Binding Sites List in 1k90
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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca802

b:0.1
occ:1.00
 O E:GLN135 2.1 91.0 1.0
OE1 E:GLU140 2.3 81.4 1.0
OE2 E:GLU140 2.6 99.6 1.0
OD1 E:ASP133 2.7 0.8 1.0
OD2 E:ASP133 2.7 0.3 1.0
CD E:GLU140 2.8 0.2 1.0
CG E:ASP133 3.0 0.0 1.0
C E:GLN135 3.1 0.4 1.0
OD1 E:ASP129 3.4 0.1 1.0
CG E:ASP129 3.6 0.1 1.0
OD2 E:ASP129 3.7 0.7 1.0
CA E:VAL136 3.7 0.9 1.0
N E:VAL136 3.8 0.3 1.0
CB E:ASP131 4.1 0.6 1.0
CA E:GLN135 4.2 0.4 1.0
N E:ASP131 4.2 0.2 1.0
N E:GLN135 4.3 0.9 1.0
CG E:GLU140 4.3 0.4 1.0
N E:ILE130 4.4 90.6 1.0
CG E:ASP131 4.4 0.0 1.0
N E:ASN137 4.5 0.4 1.0
CB E:ASP133 4.5 0.0 1.0
OD1 E:ASP131 4.5 0.6 1.0
CA E:ASP129 4.5 0.2 1.0
N E:ASP133 4.5 0.0 1.0
C E:VAL136 4.6 96.1 1.0
ND2 E:ASN137 4.6 0.3 1.0
CB E:ASP129 4.6 0.8 1.0
N E:GLY132 4.6 0.6 1.0
CA E:ASP131 4.6 0.4 1.0
CB E:GLN135 4.7 0.4 1.0
CB E:VAL136 4.9 0.8 1.0
CB E:GLU140 4.9 97.3 1.0
CA E:ASP133 5.0 0.0 1.0
CG2 E:VAL136 5.0 0.9 1.0

Calcium binding site 4 out of 6 in 1k90

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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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca803

b:83.9
occ:1.00
 OD1 E:ASP93 2.3 0.9 1.0
OD1 E:ASP95 2.4 0.9 1.0
OD1 E:ASN97 2.4 75.7 1.0
OE2 E:GLU104 2.5 0.6 1.0
OD2 E:ASP95 2.6 94.0 1.0
O E:TYR99 2.7 53.5 1.0
CG E:ASP95 2.8 0.4 1.0
OE1 E:GLU104 2.8 74.8 1.0
CD E:GLU104 3.0 0.1 1.0
CG E:ASN97 3.3 99.0 1.0
CG E:ASP93 3.4 78.4 1.0
C E:TYR99 3.9 78.7 1.0
CB E:ASN97 4.0 87.3 1.0
OG E:SER101 4.0 0.6 1.0
N E:ASN97 4.1 90.0 1.0
N E:ASP95 4.1 97.4 1.0
CB E:ASP95 4.1 89.9 1.0
CA E:ASP93 4.2 78.1 1.0
CB E:ASP93 4.2 55.5 1.0
OD2 E:ASP93 4.2 63.0 1.0
ND2 E:ASN97 4.3 86.4 1.0
CG E:GLU104 4.3 0.3 1.0
N E:GLY96 4.4 72.6 1.0
N E:LYS94 4.5 62.5 1.0
C E:ASP93 4.5 68.4 1.0
CA E:ASP95 4.5 89.1 1.0
N E:TYR99 4.6 72.1 1.0
C E:ASP95 4.6 91.1 1.0
CA E:ASN97 4.6 81.4 1.0
CA E:ILE100 4.7 0.4 1.0
N E:ILE100 4.7 74.2 1.0
N E:SER101 4.7 0.0 1.0
CA E:TYR99 4.8 85.4 1.0
NE2 E:GLN135 4.8 0.1 1.0
N E:GLY98 5.0 88.5 1.0

Calcium binding site 5 out of 6 in 1k90

Go back to Calcium Binding Sites List in 1k90
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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca804

b:67.8
occ:1.00
 OD2 F:ASP133 2.2 0.1 1.0
OE2 F:GLU140 2.2 28.6 1.0
OD1 F:ASP131 2.4 74.3 1.0
OD1 F:ASP133 2.5 67.8 1.0
O F:GLN135 2.5 56.3 1.0
CG F:ASP133 2.5 0.8 1.0
OE1 F:GLU140 2.6 69.5 1.0
CD F:GLU140 2.7 30.6 1.0
OD1 F:ASP129 3.2 65.7 1.0
CG F:ASP131 3.3 88.8 1.0
CG F:ASP129 3.5 75.2 1.0
OD2 F:ASP131 3.7 69.8 1.0
C F:GLN135 3.7 55.4 1.0
OD2 F:ASP129 3.7 54.5 1.0
CB F:ASP133 3.9 61.1 1.0
N F:ASP133 3.9 85.4 1.0
N F:ILE130 4.1 48.4 1.0
N F:ASP131 4.1 82.3 1.0
CG F:GLU140 4.2 34.3 1.0
CA F:ASP129 4.2 49.2 1.0
CB F:ASP129 4.3 46.8 1.0
N F:GLY132 4.3 35.2 1.0
N F:GLN135 4.3 68.8 1.0
CA F:ASP133 4.4 82.9 1.0
CA F:VAL136 4.4 72.7 1.0
N F:VAL136 4.5 32.3 1.0
N F:ASN137 4.6 53.2 1.0
N F:GLY134 4.6 63.8 1.0
CB F:ASP131 4.6 0.1 1.0
C F:ASP129 4.6 37.8 1.0
CA F:GLN135 4.7 52.0 1.0
CA F:ASP131 4.7 45.7 1.0
C F:ASP131 4.8 46.9 1.0
C F:GLY132 4.9 60.8 1.0
C F:ASP133 5.0 63.3 1.0

Calcium binding site 6 out of 6 in 1k90

Go back to Calcium Binding Sites List in 1k90
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 and 3' Deoxy-Atp


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 and 3' Deoxy-Atp within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca805

b:63.5
occ:1.00
 O F:TYR99 2.2 39.0 1.0
OD1 F:ASP93 2.3 54.6 1.0
OD1 F:ASN97 2.3 56.4 1.0
OE1 F:GLU104 2.5 81.8 1.0
OE2 F:GLU104 2.8 71.2 1.0
OD1 F:ASP95 2.8 81.8 1.0
CD F:GLU104 2.9 87.0 1.0
OD2 F:ASP95 3.0 78.9 1.0
CG F:ASP95 3.2 75.4 1.0
CG F:ASP93 3.4 36.8 1.0
CG F:ASN97 3.4 99.4 1.0
C F:TYR99 3.5 61.9 1.0
CA F:ASP93 4.0 58.6 1.0
ND2 F:ASN97 4.1 89.3 1.0
N F:SER101 4.2 74.5 1.0
CB F:ASP93 4.2 41.7 1.0
CG F:GLU104 4.2 99.1 1.0
CA F:ILE100 4.2 48.4 1.0
OD2 F:ASP93 4.2 51.6 1.0
N F:ILE100 4.3 44.4 1.0
N F:TYR99 4.4 67.0 1.0
N F:ASN97 4.4 62.9 1.0
C F:ASP93 4.4 72.4 1.0
CA F:TYR99 4.5 58.7 1.0
N F:ASP95 4.5 60.9 1.0
N F:LYS94 4.5 43.5 1.0
CB F:ASP95 4.6 49.3 1.0
N F:GLY96 4.6 60.6 1.0
CB F:ASN97 4.6 86.9 1.0
C F:ILE100 4.6 73.4 1.0
CB F:SER101 4.8 61.9 1.0
OG F:SER101 4.8 64.1 1.0
CB F:TYR99 4.9 65.8 1.0
CA F:ASP95 5.0 62.0 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 11:10:01 2024

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