Calcium in PDB 1s26: Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

Enzymatic activity of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site

All present enzymatic activity of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site:
4.6.1.1;

Protein crystallography data

The structure of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site, PDB code: 1s26 was solved by Y.Shen, N.L.Zhukovskaya, A.Bohm, W.-J.Tang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.78 / 3.00
Space group I 2 2 2
Cell size a, b, c (Å), α, β, γ (°) 117.555, 167.605, 345.346, 90.00, 90.00, 90.00
R / Rfree (%) 26.4 / 30.4

Other elements in 1s26:

The structure of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site also contains other interesting chemical elements:

Ytterbium (Yb) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site (pdb code 1s26). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site, PDB code: 1s26:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 1s26

Go back to Calcium Binding Sites List in 1s26
Calcium binding site 1 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca800

b:57.8
occ:1.00
 OD1 D:ASP133 1.9 64.1 1.0
OD1 D:ASP131 2.3 71.8 1.0
O D:GLN135 2.3 47.9 1.0
OE2 D:GLU140 2.4 57.4 1.0
OE1 D:GLU140 2.7 63.7 1.0
CD D:GLU140 2.8 59.5 1.0
CG D:ASP133 3.0 63.8 1.0
OD1 D:ASP129 3.4 68.2 1.0
CG D:ASP131 3.4 68.9 1.0
OD2 D:ASP133 3.5 63.9 1.0
CG D:ASP129 3.5 66.1 1.0
C D:GLN135 3.5 49.4 1.0
OD2 D:ASP129 3.5 67.0 1.0
OD2 D:ASP131 4.0 69.9 1.0
N D:ASP133 4.0 62.0 1.0
N D:ASP131 4.2 63.2 1.0
N D:ILE130 4.2 64.8 1.0
CB D:ASP133 4.2 62.3 1.0
CA D:VAL136 4.3 52.8 1.0
N D:GLN135 4.3 52.9 1.0
CG D:GLU140 4.3 58.3 1.0
CA D:ASP129 4.3 65.6 1.0
N D:VAL136 4.3 51.0 1.0
CB D:ASP129 4.4 65.0 1.0
N D:GLY132 4.5 64.6 1.0
CA D:GLN135 4.5 50.2 1.0
CA D:ASP133 4.6 61.0 1.0
CB D:ASP131 4.6 67.5 1.0
N D:ASN137 4.7 52.0 1.0
CA D:ASP131 4.7 65.2 1.0
C D:ASP131 4.8 64.8 1.0
C D:ASP129 4.8 65.5 1.0
N D:GLY134 4.8 55.1 1.0
C D:ASP133 5.0 59.0 1.0
C D:VAL136 5.0 53.0 1.0

Calcium binding site 2 out of 6 in 1s26

Go back to Calcium Binding Sites List in 1s26
Calcium binding site 2 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca801

b:58.5
occ:1.00
 OD1 D:ASN97 2.1 49.3 1.0
O D:TYR99 2.2 50.0 1.0
OD1 D:ASP95 2.4 53.1 1.0
OE1 D:GLU104 2.5 51.4 1.0
OD1 D:ASP93 2.6 58.1 1.0
OE2 D:GLU104 2.7 54.9 1.0
CD D:GLU104 2.8 55.1 1.0
CG D:ASN97 3.2 49.5 1.0
C D:TYR99 3.4 50.9 1.0
CG D:ASP95 3.4 52.6 1.0
CG D:ASP93 3.6 58.7 1.0
ND2 D:ASN97 3.7 49.9 1.0
OD2 D:ASP95 3.8 58.2 1.0
CG D:GLU104 4.1 57.4 1.0
CA D:ASP93 4.2 55.7 1.0
N D:SER101 4.2 52.6 1.0
N D:ILE100 4.3 49.8 1.0
CA D:ILE100 4.3 50.1 1.0
CB D:ASP93 4.3 56.8 1.0
N D:TYR99 4.3 54.2 1.0
CA D:TYR99 4.4 52.7 1.0
CB D:ASN97 4.4 50.2 1.0
OD2 D:ASP93 4.5 61.0 1.0
C D:ASP93 4.6 56.2 1.0
OG D:SER101 4.6 48.7 1.0
N D:ASP95 4.6 54.4 1.0
CB D:SER101 4.6 51.9 1.0
N D:ASN97 4.6 51.1 1.0
C D:ILE100 4.7 50.9 1.0
CB D:ASP95 4.7 52.6 1.0
CB D:TYR99 4.7 53.1 1.0
N D:LYS94 4.8 58.0 1.0

Calcium binding site 3 out of 6 in 1s26

Go back to Calcium Binding Sites List in 1s26
Calcium binding site 3 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca802

b:93.6
occ:1.00
 O E:GLN135 1.9 89.2 1.0
OD1 E:ASP133 2.1 0.0 1.0
OE1 E:GLU140 2.4 83.0 1.0
OE2 E:GLU140 2.5 81.2 1.0
OD1 E:ASP131 2.6 0.5 1.0
CD E:GLU140 2.8 83.0 1.0
CG E:ASP133 3.1 0.7 1.0
C E:GLN135 3.1 90.6 1.0
OD2 E:ASP133 3.5 0.8 1.0
OD2 E:ASP129 3.6 95.0 1.0
CG E:ASP129 3.6 95.1 1.0
OD1 E:ASP129 3.7 92.1 1.0
CG E:ASP131 3.8 0.1 1.0
CA E:VAL136 3.8 88.4 1.0
N E:VAL136 3.9 89.5 1.0
N E:GLN135 4.1 92.8 1.0
CA E:GLN135 4.2 91.8 1.0
CG E:GLU140 4.2 81.8 1.0
CA E:ASP129 4.2 97.8 1.0
CB E:ASP129 4.3 96.1 1.0
N E:ASP133 4.3 98.7 1.0
OD2 E:ASP131 4.3 0.7 1.0
N E:ASN137 4.3 86.3 1.0
N E:ILE130 4.3 97.0 1.0
CB E:ASP133 4.5 99.1 1.0
N E:ASP131 4.5 99.1 1.0
C E:VAL136 4.6 87.2 1.0
CA E:ASP133 4.8 98.0 1.0
N E:GLY132 4.8 98.1 1.0
C E:ASP129 4.8 97.7 1.0
ND2 E:ASN137 4.9 86.0 1.0
N E:GLY134 4.9 96.0 1.0
CG E:GLN135 4.9 93.3 1.0
CB E:GLN135 4.9 92.1 1.0
CB E:VAL136 5.0 89.0 1.0

Calcium binding site 4 out of 6 in 1s26

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Calcium binding site 4 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca803

b:84.7
occ:1.00
 O E:TYR99 2.1 77.8 1.0
OD1 E:ASN97 2.1 79.1 1.0
OE1 E:GLU104 2.3 80.2 1.0
OD1 E:ASP95 2.4 75.7 1.0
OE2 E:GLU104 2.6 80.2 1.0
OD1 E:ASP93 2.6 67.7 1.0
CD E:GLU104 2.7 81.0 1.0
CG E:ASN97 3.2 79.2 1.0
C E:TYR99 3.3 80.0 1.0
CG E:ASP95 3.4 76.2 1.0
CG E:ASP93 3.6 66.8 1.0
ND2 E:ASN97 3.8 80.1 1.0
OD2 E:ASP95 3.8 75.9 1.0
CA E:ASP93 4.0 66.5 1.0
CG E:GLU104 4.1 82.4 1.0
N E:SER101 4.1 83.4 1.0
N E:ILE100 4.2 80.8 1.0
CA E:ILE100 4.2 82.1 1.0
CB E:ASP93 4.2 66.2 1.0
CA E:TYR99 4.3 80.0 1.0
N E:TYR99 4.3 79.2 1.0
OD2 E:ASP93 4.4 64.8 1.0
C E:ASP93 4.4 66.8 1.0
CB E:ASN97 4.4 78.2 1.0
C E:ILE100 4.6 83.2 1.0
N E:ASP95 4.6 74.1 1.0
N E:ASN97 4.7 77.9 1.0
CB E:SER101 4.7 83.8 1.0
CB E:TYR99 4.7 80.9 1.0
N E:LYS94 4.7 68.4 1.0
CB E:ASP95 4.7 74.9 1.0
OG E:SER101 4.8 82.6 1.0
O E:ASP93 5.0 67.8 1.0

Calcium binding site 5 out of 6 in 1s26

Go back to Calcium Binding Sites List in 1s26
Calcium binding site 5 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca804

b:58.2
occ:1.00
 OD1 F:ASP133 2.1 74.7 1.0
O F:GLN135 2.1 62.0 1.0
OE2 F:GLU140 2.3 49.3 1.0
OE1 F:GLU140 2.4 52.4 1.0
OD1 F:ASP131 2.4 75.7 1.0
CD F:GLU140 2.7 50.9 1.0
CG F:ASP133 3.0 75.3 1.0
C F:GLN135 3.3 64.4 1.0
OD2 F:ASP133 3.4 75.2 1.0
CG F:ASP131 3.6 74.8 1.0
OD1 F:ASP129 3.8 66.6 1.0
CG F:ASP129 3.8 67.4 1.0
OD2 F:ASP129 3.8 66.3 1.0
CA F:VAL136 4.0 63.6 1.0
OD2 F:ASP131 4.1 75.5 1.0
N F:VAL136 4.1 63.6 1.0
CG F:GLU140 4.1 52.6 1.0
N F:GLN135 4.3 68.7 1.0
N F:ASN137 4.3 61.0 1.0
CA F:ASP129 4.3 69.4 1.0
N F:ILE130 4.4 68.6 1.0
N F:ASP133 4.4 73.1 1.0
CA F:GLN135 4.4 66.4 1.0
CB F:ASP133 4.4 74.7 1.0
N F:ASP131 4.4 69.3 1.0
CB F:ASP129 4.5 67.8 1.0
C F:VAL136 4.6 62.7 1.0
N F:GLY132 4.8 69.7 1.0
CB F:ASP131 4.8 72.6 1.0
ND2 F:ASN137 4.8 60.4 1.0
CA F:ASP133 4.9 73.3 1.0
C F:ASP129 4.9 69.8 1.0
CG F:GLN135 5.0 69.0 1.0

Calcium binding site 6 out of 6 in 1s26

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Calcium binding site 6 out of 6 in the Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of Anthrax Edema Factor-Calmodulin-Alpha,Beta- Methyleneadenosine 5'-Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca805

b:66.8
occ:1.00
 OD1 F:ASN97 2.0 64.7 1.0
O F:TYR99 2.1 62.8 1.0
OD1 F:ASP95 2.4 71.0 1.0
OE1 F:GLU104 2.4 75.8 1.0
OD1 F:ASP93 2.4 56.8 1.0
OE2 F:GLU104 2.8 73.1 1.0
CD F:GLU104 2.8 75.1 1.0
CG F:ASN97 3.1 65.5 1.0
C F:TYR99 3.3 63.1 1.0
CG F:ASP93 3.4 58.5 1.0
CG F:ASP95 3.5 69.0 1.0
ND2 F:ASN97 3.7 66.5 1.0
OD2 F:ASP95 3.8 69.4 1.0
CA F:ASP93 4.0 59.1 1.0
CB F:ASP93 4.1 58.3 1.0
N F:ILE100 4.2 63.4 1.0
N F:TYR99 4.2 63.9 1.0
CG F:GLU104 4.2 75.5 1.0
CA F:TYR99 4.2 63.0 1.0
OD2 F:ASP93 4.2 59.3 1.0
CA F:ILE100 4.2 63.1 1.0
N F:SER101 4.2 65.3 1.0
CB F:ASN97 4.3 64.1 1.0
C F:ASP93 4.4 60.8 1.0
N F:ASN97 4.5 64.1 1.0
N F:ASP95 4.6 65.1 1.0
CB F:TYR99 4.7 63.5 1.0
C F:ILE100 4.7 64.6 1.0
N F:LYS94 4.7 62.8 1.0
CB F:ASP95 4.8 66.2 1.0
CB F:SER101 4.8 63.6 1.0
OG F:SER101 4.9 60.8 1.0
O F:ASP93 4.9 61.7 1.0
CA F:ASN97 5.0 63.0 1.0
N F:GLY96 5.0 65.3 1.0

Reference:

Y.Shen, Q.Guo, N.L.Zhukovskaya, C.L.Drum, A.Bohm, W.-J.Tang. Structure of Anthrax Edema Factor-Calmodulin-Adenosine-5'-(Alpha,Beta-Methylene) -Triphosphate Complex Reveals An Alternative Mode of Atp Binding to the Catalytic Site Biochem.Biophys.Res.Commun. V. 317 309 2004.
ISSN: ISSN 0006-291X
PubMed: 15063758
DOI: 10.1016/J.BBRC.2004.03.046
Page generated: Sat Dec 12 03:18:37 2020

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