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Calcium in PDB 3df0: Calcium-Dependent Complex Between M-Calpain and Calpastatin

Enzymatic activity of Calcium-Dependent Complex Between M-Calpain and Calpastatin

All present enzymatic activity of Calcium-Dependent Complex Between M-Calpain and Calpastatin:
3.4.22.53;

Protein crystallography data

The structure of Calcium-Dependent Complex Between M-Calpain and Calpastatin, PDB code: 3df0 was solved by T.Moldoveanu, K.Gehring, D.R.Green, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.15 / 2.95
Space group P 42
Cell size a, b, c (Å), α, β, γ (°) 147.390, 147.390, 47.222, 90.00, 90.00, 90.00
R / Rfree (%) 22.9 / 29.9

Calcium Binding Sites:

The binding sites of Calcium atom in the Calcium-Dependent Complex Between M-Calpain and Calpastatin (pdb code 3df0). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Calcium-Dependent Complex Between M-Calpain and Calpastatin, PDB code: 3df0:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 3df0

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Calcium binding site 1 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca715

b:96.1
occ:1.00
 OD1 A:ASP96 2.3 93.4 1.0
O A:GLY91 2.4 96.4 1.0
OE2 A:GLU175 2.5 0.2 1.0
O A:ILE89 2.6 95.3 1.0
OD2 A:ASP96 2.6 92.3 1.0
CG A:ASP96 2.8 95.4 1.0
OE1 A:GLU175 2.9 0.6 1.0
CD A:GLU175 3.1 0.7 1.0
O A:GLY90 3.4 95.8 1.0
C A:GLY91 3.6 96.4 1.0
C A:ILE89 3.7 95.3 1.0
C A:GLY90 3.8 96.0 1.0
N A:THR93 4.0 96.8 1.0
OG1 A:THR93 4.1 95.8 1.0
CB A:ASP96 4.3 96.3 1.0
CA A:ALA92 4.3 96.4 1.0
N A:GLY91 4.4 96.2 1.0
N A:ILE89 4.4 95.7 1.0
CA A:GLY90 4.4 95.6 1.0
N A:ALA92 4.4 96.2 1.0
N A:GLY90 4.5 95.4 1.0
CG2 A:THR93 4.6 96.8 1.0
CA A:GLY91 4.6 96.5 1.0
CG A:GLU175 4.6 0.3 1.0
CA A:ILE89 4.6 95.4 1.0
NE1 A:TRP177 4.7 0.8 1.0
C A:ALA92 4.7 96.7 1.0
CB A:THR93 4.8 96.7 1.0
CA A:THR93 4.9 97.0 1.0
CG2 A:ILE89 4.9 95.2 1.0

Calcium binding site 2 out of 10 in 3df0

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Calcium binding site 2 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca716

b:0.5
occ:1.00
 OD2 A:ASP299 2.4 0.4 1.0
O A:GLU323 2.4 0.0 1.0
O A:GLN319 2.5 0.8 1.0
OE2 A:GLU292 2.5 84.9 1.0
OE1 A:GLU292 2.5 85.1 1.0
CD A:GLU292 2.8 87.2 1.0
OD1 A:ASP321 3.0 97.7 1.0
CG A:ASP299 3.1 0.6 1.0
OD1 A:ASP299 3.4 0.0 1.0
C A:GLN319 3.6 0.4 1.0
C A:GLU323 3.6 99.6 1.0
N A:GLN319 4.1 0.3 1.0
CG A:ASP321 4.2 98.2 1.0
CB A:ASP299 4.3 0.0 1.0
CG A:GLU292 4.3 87.7 1.0
CA A:GLU323 4.3 99.1 1.0
N A:GLU323 4.4 99.2 1.0
CA A:GLN319 4.4 0.8 1.0
N A:ASP321 4.4 99.7 1.0
N A:GLU320 4.4 0.8 1.0
CA A:GLU320 4.5 0.5 1.0
N A:PHE324 4.5 99.8 1.0
CB A:GLU323 4.6 98.8 1.0
OD2 A:ASP321 4.6 97.6 1.0
CA A:PHE324 4.7 99.8 1.0
OE2 A:GLU317 4.9 0.2 1.0
C A:ARG318 5.0 0.7 1.0
C A:GLU320 5.0 0.2 1.0

Calcium binding site 3 out of 10 in 3df0

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Calcium binding site 3 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca717

b:0.4
occ:1.00
 OD1 A:ASP545 2.1 99.6 1.0
O A:GLU547 2.2 98.8 1.0
OE1 A:GLU552 2.4 95.2 1.0
O A:ALA542 2.5 0.3 1.0
CG A:ASP545 2.9 0.6 1.0
CD A:GLU552 3.1 94.9 1.0
OE2 A:GLU552 3.2 94.5 1.0
C A:GLU547 3.2 98.5 1.0
C A:ALA542 3.3 0.6 1.0
OD2 A:ASP545 3.3 99.5 1.0
CA A:ALA542 3.5 0.1 1.0
N A:ALA546 3.6 0.9 1.0
CA A:ILE548 3.7 96.6 1.0
C A:ASP545 3.8 0.3 1.0
CB A:ALA542 3.8 0.2 1.0
N A:ILE548 3.9 97.6 1.0
C A:ALA546 3.9 99.9 1.0
N A:GLU547 4.0 99.4 1.0
CB A:ASP545 4.1 0.4 1.0
CA A:ASP545 4.1 0.6 1.0
N A:SER549 4.1 95.5 1.0
N A:ASP545 4.1 0.4 1.0
CA A:ALA546 4.2 0.3 1.0
CA A:GLU547 4.3 99.0 1.0
O A:ALA546 4.3 99.9 1.0
O A:ASP545 4.4 0.1 1.0
N A:GLY543 4.4 1.0 1.0
C A:ILE548 4.4 96.1 1.0
CG A:GLU552 4.6 93.8 1.0
CG1 A:ILE548 4.7 96.6 1.0
C A:GLY543 4.8 0.5 1.0
O A:GLY543 4.8 0.4 1.0
CB A:ILE548 4.8 96.6 1.0
N A:ALA542 4.9 0.8 1.0
C A:GLU544 5.0 0.4 1.0
CA A:GLY543 5.0 0.1 1.0

Calcium binding site 4 out of 10 in 3df0

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Calcium binding site 4 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca718

b:0.7
occ:1.00
 OD1 A:ASP585 2.4 99.2 1.0
OD2 A:ASP587 2.5 0.9 1.0
O A:LYS591 2.5 97.3 1.0
OE2 A:GLU596 2.7 96.3 1.0
OG A:SER589 2.8 97.0 1.0
OE1 A:GLU596 2.8 95.3 1.0
OE2 A:GLU547 2.8 99.0 1.0
CD A:GLU596 3.1 95.5 1.0
CG A:ASP587 3.3 0.2 1.0
OD1 A:ASP587 3.5 0.7 1.0
CG A:ASP585 3.6 0.1 1.0
O A:SER589 3.6 98.0 1.0
C A:LYS591 3.7 97.4 1.0
CD A:GLU547 3.8 99.1 1.0
CB A:SER589 3.9 97.9 1.0
OE1 A:GLU547 4.0 99.0 1.0
N A:SER589 4.1 99.1 1.0
C A:SER589 4.1 98.1 1.0
CA A:SER589 4.2 98.1 1.0
N A:LYS591 4.4 97.5 1.0
OD2 A:ASP585 4.4 97.5 1.0
CA A:ASP585 4.5 0.8 1.0
CB A:ASP585 4.5 0.3 1.0
N A:GLY593 4.5 97.3 1.0
N A:LEU592 4.6 97.5 1.0
N A:GLY588 4.6 0.5 1.0
CG A:GLU596 4.6 95.2 1.0
CA A:LEU592 4.6 97.6 1.0
CA A:LYS591 4.7 97.2 1.0
CB A:ASP587 4.7 0.1 1.0
C A:GLY588 4.8 0.0 1.0
C A:ASP585 4.9 0.5 1.0

Calcium binding site 5 out of 10 in 3df0

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Calcium binding site 5 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca719

b:71.7
occ:1.00
 O A:THR621 2.3 82.7 1.0
OD1 A:ASP615 2.4 77.0 1.0
OG A:SER619 2.4 85.0 1.0
OE1 A:GLU626 2.4 84.7 1.0
OD1 A:ASP617 2.6 85.9 1.0
OE2 A:GLU626 2.8 85.8 1.0
CD A:GLU626 3.0 84.7 1.0
CG A:ASP617 3.5 83.9 1.0
C A:THR621 3.5 82.2 1.0
CB A:SER619 3.5 82.1 1.0
CG A:ASP615 3.5 81.5 1.0
OD2 A:ASP617 3.6 85.0 1.0
OG1 A:THR621 3.8 80.8 1.0
ND2 A:ASN623 4.2 81.6 1.0
OD2 A:ASP615 4.2 76.6 1.0
N A:THR621 4.3 81.5 1.0
N A:ASN623 4.3 81.3 1.0
N A:MET622 4.4 82.2 1.0
CA A:THR621 4.4 81.3 1.0
CA A:MET622 4.4 82.3 1.0
N A:SER619 4.4 81.6 1.0
CG A:GLU626 4.5 83.0 1.0
CA A:SER619 4.5 82.1 1.0
CB A:ASP615 4.6 83.0 1.0
CA A:ASP615 4.6 83.5 1.0
CB A:THR621 4.7 80.8 1.0
CE A:MET622 4.8 87.8 1.0
N A:GLY620 4.8 81.9 1.0
CG A:ASN623 4.8 82.5 1.0
CB A:ASP617 4.8 82.3 1.0
C A:MET622 4.8 81.6 1.0
N A:ASP617 5.0 82.7 1.0
CB A:ASN623 5.0 81.1 1.0

Calcium binding site 6 out of 10 in 3df0

Go back to Calcium Binding Sites List in 3df0
Calcium binding site 6 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca720

b:72.5
occ:1.00
 OD1 A:ASP658 2.1 79.0 1.0
OD1 A:ASN661 2.5 85.0 1.0
OD1 A:ASP660 2.5 86.5 1.0
OD2 A:ASP660 2.6 85.2 1.0
CB A:ASP570 2.7 91.5 1.0
CG A:ASP658 2.9 80.0 1.0
CG A:ASP660 2.9 84.8 1.0
OD2 A:ASP658 3.0 83.9 1.0
OD2 A:ASP570 3.3 93.8 1.0
CG A:ASP570 3.5 92.7 1.0
CG A:ASN661 3.6 82.6 1.0
N A:ASP570 3.9 91.2 1.0
CA A:ASP570 4.0 91.5 1.0
OD1 B:ASP144 4.0 99.9 1.0
N A:ASN661 4.2 82.6 1.0
CB A:ASP658 4.3 78.6 1.0
ND2 A:ASN661 4.4 83.0 1.0
CB A:ASP660 4.4 83.3 1.0
CB A:ASN661 4.6 82.0 1.0
O A:GLY571 4.7 93.3 1.0
OD1 A:ASP570 4.7 95.2 1.0
C A:ASP570 4.9 91.5 1.0
CA A:ASN661 5.0 82.4 1.0

Calcium binding site 7 out of 10 in 3df0

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Calcium binding site 7 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca601

b:0.1
occ:1.00
 OD1 B:ASP114 2.3 0.1 1.0
OE2 B:GLU121 2.5 91.8 1.0
O B:GLU116 2.6 99.3 1.0
O B:ALA111 2.7 0.7 1.0
OE1 B:GLU121 3.2 92.3 1.0
CD B:GLU121 3.3 91.8 1.0
CG B:ASP114 3.3 0.2 1.0
OD2 B:ASP114 3.5 0.5 1.0
C B:ALA111 3.7 0.7 1.0
C B:GLU116 3.8 99.2 1.0
CA B:GLY112 4.1 0.6 1.0
N B:GLY112 4.3 0.6 1.0
N B:SER118 4.4 94.8 1.0
N B:GLU116 4.6 0.7 1.0
N B:VAL117 4.7 97.9 1.0
CA B:VAL117 4.7 96.5 1.0
N B:ASP114 4.7 1.0 1.0
CB B:ASP114 4.7 0.8 1.0
CB B:SER118 4.7 94.0 1.0
CG B:GLU121 4.7 90.1 1.0
N B:ASP113 4.7 0.5 1.0
CA B:GLU116 4.8 99.8 1.0
C B:GLY112 4.8 0.5 1.0
CD B:LYS160 4.8 91.1 1.0
C B:VAL117 4.9 95.7 1.0
CA B:ALA111 4.9 0.7 1.0
OG B:SER118 4.9 93.8 1.0

Calcium binding site 8 out of 10 in 3df0

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Calcium binding site 8 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca602

b:94.0
occ:1.00
 O B:LYS160 2.1 92.0 1.0
OE1 B:GLU165 2.5 91.7 1.0
OD1 B:ASP156 2.6 96.8 1.0
OG1 B:THR158 2.9 92.7 1.0
OD1 B:ASP154 2.9 95.3 1.0
OE2 B:GLU116 2.9 0.3 1.0
N B:GLY162 3.2 91.5 1.0
CD B:GLU165 3.2 91.5 1.0
C B:LYS160 3.3 91.8 1.0
OD2 B:ASP156 3.3 96.4 1.0
CG B:ASP156 3.3 95.7 1.0
OE2 B:GLU165 3.5 92.2 1.0
CA B:LEU161 3.6 91.2 1.0
CD B:GLU116 3.6 0.0 1.0
OE1 B:GLU116 3.7 0.3 1.0
C B:LEU161 3.8 91.6 1.0
N B:LEU161 3.8 91.6 1.0
CG B:ASP154 4.0 96.1 1.0
CB B:THR158 4.2 92.2 1.0
CA B:GLY162 4.2 91.0 1.0
CG B:GLU165 4.4 89.1 1.0
N B:THR158 4.5 92.7 1.0
CA B:LYS160 4.5 91.6 1.0
CB B:GLU165 4.5 87.7 1.0
CA B:ASP154 4.6 94.8 1.0
N B:LYS160 4.6 91.4 1.0
CB B:ASP154 4.6 94.7 1.0
CG2 B:THR158 4.6 91.7 1.0
CA B:THR158 4.7 92.4 1.0
CB B:ASP156 4.8 94.5 1.0
N B:SER155 4.8 94.7 1.0
CG B:GLU116 4.9 0.1 1.0
CB B:LEU161 4.9 91.1 1.0
N B:ASP156 4.9 94.8 1.0
O B:LEU161 5.0 92.1 1.0
C B:THR158 5.0 92.3 1.0

Calcium binding site 9 out of 10 in 3df0

Go back to Calcium Binding Sites List in 3df0
Calcium binding site 9 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca603

b:80.0
occ:1.00
 O B:THR190 2.2 89.9 1.0
OG B:SER188 2.4 89.9 1.0
OD1 B:ASP186 2.5 90.5 1.0
OE1 B:GLU195 2.5 88.8 1.0
OD2 B:ASP184 2.5 86.7 1.0
OE2 B:GLU195 2.7 90.5 1.0
CD B:GLU195 3.0 89.7 1.0
CG B:ASP186 3.3 90.0 1.0
C B:THR190 3.5 89.7 1.0
OD2 B:ASP186 3.5 91.7 1.0
CB B:SER188 3.6 89.5 1.0
CG B:ASP184 3.7 88.0 1.0
N B:GLY192 4.0 90.0 1.0
OG1 B:THR190 4.0 88.7 1.0
N B:SER188 4.1 89.8 1.0
CA B:ASP184 4.3 88.6 1.0
N B:ILE191 4.3 89.3 1.0
CA B:ILE191 4.3 89.0 1.0
CB B:ASP184 4.3 88.5 1.0
CA B:SER188 4.4 89.5 1.0
N B:THR190 4.4 89.8 1.0
CA B:THR190 4.4 89.6 1.0
CG B:GLU195 4.5 91.1 1.0
N B:ASP186 4.5 88.6 1.0
C B:ILE191 4.6 89.4 1.0
OD1 B:ASP184 4.6 87.0 1.0
CB B:ASP186 4.6 88.9 1.0
OD1 B:ASN225 4.7 96.9 1.0
C B:ASP184 4.7 88.6 1.0
CA B:GLY192 4.8 90.8 1.0
N B:THR185 4.8 88.4 1.0
CB B:THR190 4.8 89.8 1.0
N B:ARG187 4.8 89.6 1.0
N B:GLY189 4.9 89.2 1.0
CA B:ASP186 4.9 88.9 1.0
C B:ASP186 5.0 89.2 1.0

Calcium binding site 10 out of 10 in 3df0

Go back to Calcium Binding Sites List in 3df0
Calcium binding site 10 out of 10 in the Calcium-Dependent Complex Between M-Calpain and Calpastatin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Calcium-Dependent Complex Between M-Calpain and Calpastatin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca604

b:87.2
occ:1.00
 OD1 B:ASN230 2.0 93.7 1.0
OD1 B:ASP227 2.2 93.0 1.0
OD1 B:ASP229 2.6 94.7 1.0
OD1 B:ASP139 2.6 0.9 1.0
OD2 B:ASP229 2.6 94.0 1.0
OD2 B:ASP139 2.7 0.5 1.0
CG B:ASP139 2.9 0.1 1.0
CG B:ASP229 3.0 93.5 1.0
CG B:ASN230 3.1 92.9 1.0
CG B:ASP227 3.2 94.6 1.0
CB B:ASP227 3.5 94.8 1.0
ND2 B:ASN230 3.7 91.1 1.0
N B:ASN230 4.2 93.8 1.0
N B:ASP139 4.2 95.6 1.0
CB B:ASP139 4.3 97.0 1.0
CB B:ASN230 4.3 93.0 1.0
OD2 B:ASP227 4.4 94.5 1.0
CB B:ASP229 4.4 92.9 1.0
O B:GLY140 4.6 94.9 1.0
CA B:ASN230 4.8 92.9 1.0
CA B:ASP139 4.8 96.5 1.0
OG1 B:THR138 4.8 94.3 1.0
C B:ASP229 4.9 93.6 1.0
CA B:ASP227 5.0 94.3 1.0
N B:ASP229 5.0 93.5 1.0

Reference:

T.Moldoveanu, K.Gehring, D.R.Green. Concerted Multi-Pronged Attack By Calpastatin to Occlude the Catalytic Cleft of Heterodimeric Calpains. Nature V. 456 404 2008.
ISSN: ISSN 0028-0836
PubMed: 19020622
DOI: 10.1038/NATURE07353
Page generated: Sat Jul 13 09:00:31 2024

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