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Calcium in PDB 3kwv: Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers

Enzymatic activity of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers

All present enzymatic activity of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers:
3.4.24.83;

Protein crystallography data

The structure of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers, PDB code: 3kwv was solved by G.K.Feld, A.F.Kintzer, B.A.Krantz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.84 / 3.10
Space group P 4 21 2
Cell size a, b, c (Å), α, β, γ (°) 178.381, 178.381, 240.363, 90.00, 90.00, 90.00
R / Rfree (%) 24.9 / 28.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers (pdb code 3kwv). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers, PDB code: 3kwv:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 3kwv

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Calcium binding site 1 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca736

b:52.7
occ:1.00
 O A:HOH738 1.9 62.7 1.0
OD1 A:ASP181 2.3 68.0 1.0
OD1 A:ASP177 2.3 57.7 1.0
O A:ILE183 2.3 57.7 1.0
OE2 A:GLU188 2.4 58.5 1.0
OD1 A:ASP179 2.4 49.2 1.0
OD2 A:ASP181 2.6 56.3 1.0
CG A:ASP181 2.7 63.3 1.0
CG A:ASP179 3.2 57.0 1.0
OD2 A:ASP179 3.4 62.0 1.0
CD A:GLU188 3.4 56.2 1.0
C A:ILE183 3.4 60.3 1.0
CG A:ASP177 3.6 72.0 1.0
N A:ILE183 3.9 59.5 1.0
CA A:ILE183 4.0 47.2 1.0
CB A:ILE183 4.0 55.1 1.0
CB A:ASP181 4.1 47.4 1.0
CA A:CA737 4.1 45.9 1.0
CG A:GLU188 4.1 55.7 1.0
N A:ASP181 4.2 54.3 1.0
O A:PRO223 4.2 65.2 1.0
OE1 A:GLU188 4.3 54.4 1.0
OD2 A:ASP177 4.3 63.2 1.0
OD1 A:ASP185 4.4 79.6 1.0
O A:PRO184 4.4 64.8 1.0
CA A:PRO223 4.5 53.9 1.0
C A:PRO184 4.5 56.5 1.0
CA A:ASP177 4.5 56.4 1.0
N A:PRO184 4.6 60.1 1.0
N A:GLY182 4.6 40.8 1.0
CA A:ASP181 4.6 46.1 1.0
N A:ASP179 4.6 63.1 1.0
CB A:ASP177 4.6 47.6 1.0
CB A:ASP179 4.7 47.9 1.0
C A:ASP177 4.7 73.1 1.0
C A:PRO223 4.7 63.1 1.0
N A:ASN180 4.8 58.7 1.0
CA A:PRO184 4.9 50.6 1.0
N A:ARG178 4.9 60.8 1.0
N A:ASP185 4.9 69.8 1.0
CG1 A:ILE183 4.9 51.1 1.0
CG2 A:ILE183 5.0 57.5 1.0
C A:ASP181 5.0 60.1 1.0

Calcium binding site 2 out of 8 in 3kwv

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Calcium binding site 2 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca737

b:45.9
occ:1.00
 O A:SER222 2.1 62.6 1.0
OD2 A:ASP179 2.3 62.0 1.0
OD2 A:ASP235 2.3 54.6 1.0
OE1 A:GLU188 2.4 54.4 1.0
O A:LYS225 2.4 55.3 1.0
OD2 A:ASP181 2.4 56.3 1.0
OE2 A:GLU188 2.7 58.5 1.0
CD A:GLU188 2.9 56.2 1.0
C A:SER222 3.4 57.5 1.0
CG A:ASP179 3.5 57.0 1.0
C A:LYS225 3.5 44.8 1.0
CG A:ASP235 3.5 59.4 1.0
CG A:ASP181 3.6 63.3 1.0
OG1 A:THR228 3.9 46.0 1.0
OD1 A:ASP179 4.1 49.2 1.0
CA A:CA736 4.1 52.7 1.0
N A:LYS225 4.1 53.7 1.0
CB A:ASP235 4.2 52.8 1.0
N A:PRO223 4.2 49.2 1.0
CA A:PRO223 4.2 53.9 1.0
CA A:LYS225 4.3 51.1 1.0
CB A:ASP181 4.3 47.4 1.0
N A:TRP226 4.4 50.9 1.0
CA A:SER222 4.4 46.5 1.0
N A:SER222 4.4 55.7 1.0
C A:PRO223 4.4 63.1 1.0
CG A:GLU188 4.4 55.7 1.0
OD1 A:ASP235 4.4 58.7 1.0
CA A:TRP226 4.5 47.1 1.0
C A:TRP226 4.5 57.4 1.0
OD1 A:ASP181 4.5 68.0 1.0
OG A:SER221 4.5 45.7 1.0
CB A:ASP179 4.6 47.9 1.0
O A:TRP226 4.7 59.5 1.0
CB A:SER221 4.8 55.2 1.0
N A:GLU224 4.8 45.6 1.0
O A:PRO223 4.8 65.2 1.0
CB A:LYS225 4.8 48.5 1.0
CB A:SER222 4.9 45.9 1.0
C A:SER221 4.9 44.8 1.0
O A:HOH738 4.9 62.7 1.0
N A:SER227 5.0 53.1 1.0
N A:THR228 5.0 50.8 1.0

Calcium binding site 3 out of 8 in 3kwv

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Calcium binding site 3 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca736

b:57.7
occ:1.00
 O B:HOH738 1.9 44.2 1.0
OD1 B:ASP177 2.3 59.2 1.0
OD1 B:ASP181 2.3 61.7 1.0
O B:ILE183 2.3 55.9 1.0
OE2 B:GLU188 2.3 52.9 1.0
OD1 B:ASP179 2.4 53.6 1.0
CG B:ASP181 2.9 56.2 1.0
OD2 B:ASP181 3.0 48.0 1.0
CG B:ASP179 3.1 57.7 1.0
OD2 B:ASP179 3.2 49.5 1.0
CD B:GLU188 3.3 56.6 1.0
C B:ILE183 3.3 62.2 1.0
CG B:ASP177 3.5 79.2 1.0
N B:ILE183 3.7 64.2 1.0
CA B:ILE183 3.9 51.5 1.0
CG B:GLU188 3.9 61.3 1.0
CB B:ILE183 4.1 48.0 1.0
CA B:CA737 4.2 48.9 1.0
OD1 B:ASP185 4.3 81.2 1.0
OE1 B:GLU188 4.3 57.0 1.0
CB B:ASP181 4.3 47.8 1.0
N B:ASP181 4.3 69.0 1.0
OD2 B:ASP177 4.4 78.7 1.0
O B:PRO223 4.4 65.1 1.0
CA B:ASP177 4.4 56.9 1.0
N B:PRO184 4.4 62.7 1.0
N B:GLY182 4.5 52.9 1.0
CB B:ASP177 4.5 56.7 1.0
C B:PRO184 4.5 60.2 1.0
CA B:PRO223 4.5 43.8 1.0
CB B:ASP179 4.6 47.8 1.0
C B:ASP177 4.6 68.2 1.0
N B:ASP179 4.6 46.9 1.0
N B:ASP185 4.7 66.6 1.0
O B:PRO184 4.7 57.7 1.0
CA B:PRO184 4.7 58.0 1.0
CA B:ASP181 4.7 62.1 1.0
N B:ASN180 4.8 52.8 1.0
C B:PRO223 4.8 52.0 1.0
C B:GLY182 4.9 66.8 1.0
N B:ARG178 4.9 50.3 1.0
CG2 B:ILE183 5.0 62.3 1.0
CA B:ASP179 5.0 38.7 1.0

Calcium binding site 4 out of 8 in 3kwv

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Calcium binding site 4 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca737

b:48.9
occ:1.00
 O B:SER222 2.2 57.5 1.0
OD2 B:ASP179 2.3 49.5 1.0
OE1 B:GLU188 2.3 57.0 1.0
OD2 B:ASP235 2.4 46.0 1.0
O B:LYS225 2.4 47.3 1.0
OD2 B:ASP181 2.4 48.0 1.0
OE2 B:GLU188 2.6 52.9 1.0
CD B:GLU188 2.8 56.6 1.0
C B:SER222 3.3 59.1 1.0
CG B:ASP179 3.4 57.7 1.0
CG B:ASP235 3.5 58.1 1.0
C B:LYS225 3.5 43.2 1.0
CG B:ASP181 3.6 56.2 1.0
OG1 B:THR228 4.1 44.1 1.0
OD1 B:ASP179 4.1 53.6 1.0
N B:PRO223 4.2 47.7 1.0
CB B:ASP235 4.2 55.5 1.0
CA B:CA736 4.2 57.7 1.0
CA B:PRO223 4.2 43.8 1.0
N B:LYS225 4.2 51.5 1.0
N B:SER222 4.2 62.0 1.0
CA B:SER222 4.3 58.7 1.0
CG B:GLU188 4.3 61.3 1.0
CA B:LYS225 4.4 51.1 1.0
CB B:ASP181 4.4 47.8 1.0
OD1 B:ASP235 4.4 62.7 1.0
CB B:ASP179 4.4 47.8 1.0
OD1 B:ASP181 4.5 61.7 1.0
C B:PRO223 4.5 52.0 1.0
N B:TRP226 4.5 61.5 1.0
OG B:SER221 4.5 56.8 1.0
CB B:SER221 4.5 71.0 1.0
CA B:TRP226 4.6 56.0 1.0
C B:TRP226 4.6 57.8 1.0
O B:TRP226 4.7 54.8 1.0
C B:SER221 4.8 61.0 1.0
N B:GLU224 4.8 58.3 1.0
CB B:LYS225 4.8 47.9 1.0
CB B:SER222 4.8 51.9 1.0
O B:HOH738 4.9 44.2 1.0
O B:PRO223 4.9 65.1 1.0
CB B:GLU188 5.0 57.5 1.0

Calcium binding site 5 out of 8 in 3kwv

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Calcium binding site 5 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca736

b:65.8
occ:1.00
 O D:HOH738 1.9 58.5 1.0
OD1 D:ASP181 2.3 65.2 1.0
O D:ILE183 2.3 62.0 1.0
OD1 D:ASP177 2.3 67.7 1.0
OE2 D:GLU188 2.4 55.3 1.0
OD1 D:ASP179 2.4 52.0 1.0
OD2 D:ASP181 2.6 59.5 1.0
CG D:ASP181 2.7 64.0 1.0
CG D:ASP179 3.3 63.2 1.0
OD2 D:ASP179 3.4 65.9 1.0
CD D:GLU188 3.4 57.1 1.0
C D:ILE183 3.4 71.3 1.0
CG D:ASP177 3.6 73.9 1.0
N D:ILE183 3.9 63.1 1.0
CA D:ILE183 4.0 55.4 1.0
CB D:ILE183 4.0 58.2 1.0
CA D:CA737 4.1 55.1 1.0
CB D:ASP181 4.1 50.4 1.0
CG D:GLU188 4.1 59.3 1.0
N D:ASP181 4.2 59.1 1.0
O D:PRO223 4.2 68.1 1.0
OE1 D:GLU188 4.3 53.4 1.0
OD2 D:ASP177 4.3 63.7 1.0
O D:PRO184 4.4 64.1 1.0
OD1 D:ASP185 4.4 78.9 1.0
C D:PRO184 4.5 61.4 1.0
CA D:ASP177 4.5 56.0 1.0
CA D:PRO223 4.5 56.9 1.0
N D:PRO184 4.6 59.7 1.0
N D:GLY182 4.6 41.9 1.0
CB D:ASP177 4.6 49.9 1.0
N D:ASP179 4.6 63.4 1.0
CA D:ASP181 4.6 52.2 1.0
CB D:ASP179 4.7 44.5 1.0
C D:ASP177 4.7 74.2 1.0
C D:PRO223 4.7 65.4 1.0
N D:ASN180 4.8 56.7 1.0
CA D:PRO184 4.8 48.2 1.0
N D:ARG178 4.9 62.0 1.0
N D:ASP185 4.9 75.3 1.0
CG1 D:ILE183 4.9 50.0 1.0
CG2 D:ILE183 5.0 60.8 1.0
C D:ASP181 5.0 66.8 1.0

Calcium binding site 6 out of 8 in 3kwv

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Calcium binding site 6 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca737

b:55.1
occ:1.00
 O D:SER222 2.2 66.6 1.0
OD2 D:ASP179 2.3 65.9 1.0
OD2 D:ASP235 2.3 51.2 1.0
OE1 D:GLU188 2.3 53.4 1.0
OD2 D:ASP181 2.3 59.5 1.0
O D:LYS225 2.4 61.9 1.0
OE2 D:GLU188 2.7 55.3 1.0
CD D:GLU188 2.9 57.1 1.0
C D:SER222 3.4 54.1 1.0
CG D:ASP179 3.4 63.2 1.0
CG D:ASP235 3.5 61.2 1.0
C D:LYS225 3.5 52.0 1.0
CG D:ASP181 3.6 64.0 1.0
OG1 D:THR228 4.0 47.8 1.0
OD1 D:ASP179 4.1 52.0 1.0
CA D:CA736 4.1 65.8 1.0
CB D:ASP235 4.1 57.5 1.0
N D:LYS225 4.2 51.5 1.0
N D:PRO223 4.2 47.5 1.0
CA D:PRO223 4.2 56.9 1.0
CB D:ASP181 4.3 50.4 1.0
CA D:LYS225 4.4 57.8 1.0
CG D:GLU188 4.4 59.3 1.0
N D:TRP226 4.4 48.7 1.0
CA D:SER222 4.4 52.8 1.0
N D:SER222 4.4 54.6 1.0
C D:PRO223 4.4 65.4 1.0
OD1 D:ASP235 4.4 68.8 1.0
OD1 D:ASP181 4.5 65.2 1.0
CA D:TRP226 4.5 45.6 1.0
OG D:SER221 4.5 56.8 1.0
C D:TRP226 4.5 51.8 1.0
CB D:ASP179 4.6 44.5 1.0
O D:TRP226 4.7 64.0 1.0
CB D:SER221 4.8 62.5 1.0
O D:PRO223 4.8 68.1 1.0
N D:GLU224 4.8 52.2 1.0
CB D:LYS225 4.8 46.5 1.0
C D:SER221 4.9 49.2 1.0
O D:HOH738 4.9 58.5 1.0
CB D:SER222 4.9 52.7 1.0
N D:SER227 5.0 47.4 1.0

Calcium binding site 7 out of 8 in 3kwv

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Calcium binding site 7 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca736

b:52.4
occ:1.00
 O E:HOH738 1.9 61.5 1.0
OD1 E:ASP181 2.3 61.5 1.0
OD1 E:ASP177 2.3 65.7 1.0
O E:ILE183 2.3 54.9 1.0
OE2 E:GLU188 2.3 40.8 1.0
OD1 E:ASP179 2.4 62.9 1.0
CG E:ASP181 2.9 56.6 1.0
OD2 E:ASP181 3.0 55.1 1.0
CG E:ASP179 3.1 59.0 1.0
OD2 E:ASP179 3.2 53.0 1.0
CD E:GLU188 3.3 53.0 1.0
C E:ILE183 3.3 63.2 1.0
CG E:ASP177 3.6 80.0 1.0
N E:ILE183 3.7 62.9 1.0
CA E:ILE183 3.9 56.0 1.0
CG E:GLU188 3.9 62.2 1.0
CB E:ILE183 4.1 51.2 1.0
CA E:CA737 4.2 48.0 1.0
OE1 E:GLU188 4.3 54.8 1.0
OD1 E:ASP185 4.3 83.8 1.0
CB E:ASP181 4.3 46.4 1.0
N E:ASP181 4.3 67.1 1.0
O E:PRO223 4.4 72.8 1.0
CA E:ASP177 4.4 58.1 1.0
OD2 E:ASP177 4.4 72.4 1.0
N E:PRO184 4.4 59.6 1.0
N E:GLY182 4.5 53.8 1.0
CB E:ASP177 4.5 60.1 1.0
C E:PRO184 4.5 62.8 1.0
CA E:PRO223 4.5 43.0 1.0
CB E:ASP179 4.6 45.9 1.0
C E:ASP177 4.6 67.6 1.0
N E:ASP179 4.6 53.3 1.0
N E:ASP185 4.7 69.2 1.0
O E:PRO184 4.7 53.9 1.0
CA E:PRO184 4.7 55.0 1.0
CA E:ASP181 4.8 60.0 1.0
N E:ASN180 4.8 58.6 1.0
C E:PRO223 4.8 53.1 1.0
C E:GLY182 4.9 70.2 1.0
N E:ARG178 4.9 48.8 1.0
CG2 E:ILE183 5.0 64.2 1.0
O E:ASP177 5.0 69.0 1.0
CA E:ASP179 5.0 44.3 1.0

Calcium binding site 8 out of 8 in 3kwv

Go back to Calcium Binding Sites List in 3kwv
Calcium binding site 8 out of 8 in the Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca737

b:48.0
occ:1.00
 O E:SER222 2.2 58.1 1.0
OD2 E:ASP179 2.3 53.0 1.0
OE1 E:GLU188 2.3 54.8 1.0
OD2 E:ASP235 2.3 49.2 1.0
O E:LYS225 2.4 46.0 1.0
OD2 E:ASP181 2.4 55.1 1.0
OE2 E:GLU188 2.6 40.8 1.0
CD E:GLU188 2.8 53.0 1.0
C E:SER222 3.3 50.7 1.0
CG E:ASP179 3.4 59.0 1.0
CG E:ASP235 3.5 60.1 1.0
C E:LYS225 3.5 44.6 1.0
CG E:ASP181 3.6 56.6 1.0
OG1 E:THR228 4.1 47.7 1.0
OD1 E:ASP179 4.1 62.9 1.0
CB E:ASP235 4.2 48.6 1.0
N E:PRO223 4.2 45.4 1.0
CA E:CA736 4.2 52.4 1.0
CA E:PRO223 4.2 43.0 1.0
N E:SER222 4.2 63.0 1.0
N E:LYS225 4.2 47.6 1.0
CA E:SER222 4.3 50.7 1.0
CG E:GLU188 4.3 62.2 1.0
CA E:LYS225 4.4 51.4 1.0
OD1 E:ASP235 4.4 59.4 1.0
CB E:ASP181 4.4 46.4 1.0
OD1 E:ASP181 4.5 61.5 1.0
CB E:ASP179 4.5 45.9 1.0
N E:TRP226 4.5 54.5 1.0
OG E:SER221 4.5 55.8 1.0
C E:PRO223 4.5 53.1 1.0
CB E:SER221 4.5 61.0 1.0
CA E:TRP226 4.6 48.7 1.0
C E:TRP226 4.6 54.2 1.0
O E:TRP226 4.6 62.5 1.0
C E:SER221 4.8 59.8 1.0
CB E:LYS225 4.8 45.5 1.0
N E:GLU224 4.8 50.7 1.0
CB E:SER222 4.8 49.1 1.0
O E:HOH738 4.9 61.5 1.0
O E:PRO223 4.9 72.8 1.0
CB E:GLU188 5.0 55.1 1.0

Reference:

G.K.Feld, K.L.Thoren, A.F.Kintzer, H.J.Sterling, I.I.Tang, S.G.Greenberg, E.R.Williams, B.A.Krantz. Structural Basis For the Unfolding of Anthrax Lethal Factor By Protective Antigen Oligomers. Nat.Struct.Mol.Biol. V. 17 1383 2010.
ISSN: ISSN 1545-9993
PubMed: 21037566
DOI: 10.1038/NSMB.1923
Page generated: Sat Jul 13 12:42:40 2024

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