Atomistry » Calcium » PDB 1jw6-1k9k » 1k90
Atomistry »
  Calcium »
    PDB 1jw6-1k9k »
      1k90 »

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

Go back to Calcium Binding Sites List in 1k90
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

Go back to Calcium Binding Sites List in 1k90
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy