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Calcium in PDB 6bkj: Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin

Enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin

All present enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin:
3.4.22.54;

Protein crystallography data

The structure of Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin, PDB code: 6bkj was solved by Q.Ye, R.L.Campbell, P.L.Davies, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.99 / 3.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.930, 106.690, 234.630, 90.00, 90.00, 90.00
R / Rfree (%) 27.7 / 35.3

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin (pdb code 6bkj). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin, PDB code: 6bkj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6bkj

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:73.2
occ:1.00
 O A:GLY115 2.3 0.5 1.0
O A:ILE113 2.5 0.5 1.0
OD2 A:ASP120 2.8 90.0 1.0
OD1 A:ASP120 2.8 94.3 1.0
OE2 A:GLU199 3.0 70.8 1.0
CG A:ASP120 3.2 91.1 1.0
OE1 A:GLU199 3.4 71.8 1.0
C A:GLY115 3.5 0.6 1.0
O A:ASP114 3.6 0.2 1.0
CD A:GLU199 3.6 72.5 1.0
ND2 A:ASN117 3.6 0.7 1.0
C A:ILE113 3.6 0.5 1.0
C A:ASP114 3.8 0.9 1.0
OD1 A:ASN117 4.0 0.1 1.0
CG A:ASN117 4.0 0.2 1.0
N A:GLY115 4.2 0.4 1.0
CA A:GLY115 4.4 0.1 1.0
N A:ASN117 4.4 95.0 1.0
N A:ASP114 4.5 1.0 1.0
CA A:ASP114 4.5 0.7 1.0
N A:ALA116 4.5 0.9 1.0
N A:ILE113 4.6 94.2 1.0
CA A:ILE113 4.6 95.7 1.0
CA A:ALA116 4.7 0.6 1.0
CB A:ASP120 4.7 87.8 1.0
CB A:ASP114 4.8 0.6 1.0
CB A:ILE113 4.9 95.3 1.0
C A:ALA116 5.0 0.6 1.0

Calcium binding site 2 out of 8 in 6bkj

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:0.2
occ:1.00
 OD2 A:ASP371 2.5 0.6 1.0
O A:GLU396 2.6 98.9 1.0
O A:THR392 2.6 0.5 1.0
OD1 A:ASP394 2.7 1.0 1.0
OE1 A:GLU364 3.0 0.2 1.0
OD1 A:ASP371 3.1 0.2 1.0
OD2 A:ASP394 3.1 0.8 1.0
CG A:ASP371 3.1 0.2 1.0
CG A:ASP394 3.2 0.7 1.0
C A:THR392 3.7 0.1 1.0
O A:GLN390 3.7 0.9 1.0
OE2 A:GLU364 3.7 0.1 1.0
C A:GLU396 3.7 0.4 1.0
CD A:GLU364 3.8 0.4 1.0
N A:THR392 4.0 0.4 1.0
CB A:THR392 4.2 0.4 1.0
CA A:THR392 4.2 0.7 1.0
N A:ASP394 4.3 0.1 1.0
N A:GLU396 4.5 99.3 1.0
CA A:GLU396 4.5 0.1 1.0
CB A:ASP394 4.5 0.5 1.0
CB A:ASP371 4.6 0.7 1.0
N A:PHE397 4.7 0.2 1.0
CB A:GLU396 4.8 0.5 1.0
CA A:PHE397 4.8 0.1 1.0
N A:GLU393 4.8 0.8 1.0
C A:GLN390 4.8 0.7 1.0
N A:GLY395 5.0 0.1 1.0
CA A:ASP394 5.0 0.4 1.0

Calcium binding site 3 out of 8 in 6bkj

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:82.7
occ:1.00
 O B:GLY115 2.3 94.4 1.0
O B:ILE113 2.6 99.0 1.0
OE2 B:GLU199 2.7 78.2 1.0
OD2 B:ASP120 2.8 78.5 1.0
OD1 B:ASP120 2.9 77.0 1.0
OE1 B:GLU199 3.2 91.2 1.0
CG B:ASP120 3.2 80.3 1.0
CD B:GLU199 3.3 81.7 1.0
O B:ASP114 3.5 0.0 1.0
C B:GLY115 3.5 1.0 1.0
C B:ILE113 3.6 94.0 1.0
ND2 B:ASN117 3.6 0.1 1.0
C B:ASP114 3.8 0.3 1.0
OD1 B:ASN117 4.0 0.4 1.0
CG B:ASN117 4.1 0.2 1.0
N B:GLY115 4.1 0.1 1.0
CA B:GLY115 4.3 0.4 1.0
N B:ASP114 4.4 0.2 1.0
N B:ASN117 4.5 0.2 1.0
CA B:ASP114 4.5 0.8 1.0
N B:ALA116 4.5 0.1 1.0
N B:ILE113 4.5 93.1 1.0
CA B:ILE113 4.6 88.7 1.0
CA B:ALA116 4.7 0.5 1.0
CB B:ASP120 4.7 79.8 1.0
CB B:ASP114 4.7 0.8 1.0
CG B:GLU199 4.8 79.9 1.0
CB B:ILE113 4.8 84.5 1.0
OG1 B:THR119 4.9 86.1 1.0
C B:ALA116 5.0 0.0 1.0

Calcium binding site 4 out of 8 in 6bkj

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:0.6
occ:1.00
 OD2 B:ASP371 2.3 0.0 1.0
O B:THR392 2.4 0.5 1.0
OD1 B:ASP394 2.4 0.8 1.0
O B:GLU396 2.7 89.5 1.0
OE2 B:GLU364 2.8 0.7 1.0
CG B:ASP394 3.0 0.6 1.0
OD2 B:ASP394 3.1 0.3 1.0
OE1 B:GLU364 3.1 0.7 1.0
CG B:ASP371 3.2 0.7 1.0
OD1 B:ASP371 3.3 0.9 1.0
CD B:GLU364 3.3 0.2 1.0
C B:THR392 3.5 0.4 1.0
C B:GLU396 3.9 99.7 1.0
N B:THR392 3.9 0.5 1.0
N B:ASP394 3.9 0.5 1.0
O B:GLN390 4.0 0.7 1.0
CA B:THR392 4.2 0.5 1.0
CB B:ASP394 4.2 0.7 1.0
N B:GLU396 4.3 0.1 1.0
N B:GLU393 4.5 0.9 1.0
CA B:GLU396 4.6 0.5 1.0
CB B:ASP371 4.6 0.6 1.0
CA B:ASP394 4.6 0.2 1.0
N B:GLY395 4.6 0.2 1.0
CB B:THR392 4.7 0.4 1.0
CA B:GLU393 4.7 0.7 1.0
CG B:GLU364 4.8 1.0 1.0
C B:GLU393 4.8 0.2 1.0
CB B:GLU396 4.9 0.1 1.0
N B:PHE397 4.9 1.0 1.0

Calcium binding site 5 out of 8 in 6bkj

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:65.3
occ:1.00
 O C:ILE113 2.3 81.5 1.0
O C:GLY115 2.3 94.3 1.0
OE2 C:GLU199 2.6 85.4 1.0
OD2 C:ASP120 2.6 0.2 1.0
OD1 C:ASP120 2.8 0.3 1.0
OD1 C:ASP114 3.0 0.2 1.0
OE1 C:GLU199 3.1 82.1 1.0
CG C:ASP120 3.1 99.7 1.0
CD C:GLU199 3.2 82.7 1.0
C C:ILE113 3.5 90.8 1.0
ND2 C:ASN117 3.5 0.6 1.0
C C:GLY115 3.5 0.4 1.0
O C:ASP114 3.9 0.1 1.0
C C:ASP114 4.0 0.5 1.0
CG C:ASP114 4.2 1.0 1.0
N C:GLY115 4.3 0.1 1.0
CA C:ILE113 4.4 83.3 1.0
N C:ILE113 4.4 87.1 1.0
CG C:ASN117 4.4 0.1 1.0
CA C:GLY115 4.5 0.9 1.0
N C:ALA116 4.5 0.0 1.0
N C:ASP114 4.5 0.7 1.0
CB C:ASP120 4.5 0.1 1.0
CA C:ALA116 4.6 0.0 1.0
CG C:GLU199 4.7 78.9 1.0
CB C:ILE113 4.7 73.5 1.0
CA C:ASP114 4.7 0.2 1.0
N C:ASN117 4.7 0.6 1.0
NE1 C:TRP201 4.9 90.8 1.0
CB C:ASN117 4.9 0.9 1.0
C C:ALA116 5.0 0.0 1.0

Calcium binding site 6 out of 8 in 6bkj

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


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 Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:94.5
occ:1.00
 O C:GLU396 2.4 89.9 1.0
OD1 C:ASP394 2.5 0.7 1.0
O C:THR392 2.5 0.5 1.0
OD2 C:ASP371 2.5 0.9 1.0
OE2 C:GLU364 2.8 0.9 1.0
OE1 C:GLU364 3.1 0.1 1.0
OD1 C:ASP371 3.2 0.2 1.0
CG C:ASP371 3.3 0.6 1.0
OG1 C:THR392 3.3 0.4 1.0
CD C:GLU364 3.3 0.5 1.0
CG C:ASP394 3.4 0.7 1.0
C C:GLU396 3.5 88.8 1.0
C C:THR392 3.6 0.2 1.0
OD2 C:ASP394 3.8 0.9 1.0
O C:GLN390 4.1 0.0 1.0
N C:GLU396 4.2 94.2 1.0
N C:THR392 4.2 0.5 1.0
N C:ASP394 4.2 0.8 1.0
CA C:GLU396 4.3 93.8 1.0
CA C:THR392 4.3 0.3 1.0
CB C:THR392 4.3 0.1 1.0
N C:PHE397 4.5 87.4 1.0
CB C:GLU396 4.6 99.4 1.0
CB C:ASP394 4.7 0.5 1.0
N C:GLU393 4.7 0.0 1.0
CB C:ASP371 4.7 0.6 1.0
CA C:PHE397 4.7 94.2 1.0
CG C:GLU364 4.8 0.1 1.0
N C:GLY395 4.8 0.3 1.0
CA C:GLU393 4.9 0.9 1.0
CA C:ASP394 4.9 0.3 1.0

Calcium binding site 7 out of 8 in 6bkj

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Calcium binding site 7 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:84.5
occ:1.00
 O D:ILE113 2.1 96.0 1.0
OE2 D:GLU199 2.5 80.4 1.0
O D:GLY115 2.6 0.1 1.0
OD2 D:ASP120 2.8 0.6 1.0
OD1 D:ASP120 2.8 97.1 1.0
OE1 D:GLU199 2.9 83.3 1.0
CD D:GLU199 3.1 82.9 1.0
CG D:ASP120 3.2 0.5 1.0
C D:ILE113 3.3 94.8 1.0
OD1 D:ASN117 3.5 0.9 1.0
C D:GLY115 3.8 0.6 1.0
O D:ASP114 3.9 0.9 1.0
C D:ASP114 4.0 0.6 1.0
CA D:ILE113 4.2 90.0 1.0
N D:ILE113 4.3 92.9 1.0
N D:ASP114 4.3 0.3 1.0
N D:GLY115 4.3 0.1 1.0
CB D:ILE113 4.4 83.9 1.0
CG D:ASN117 4.4 0.5 1.0
CG D:GLU199 4.5 84.4 1.0
CA D:ASP114 4.5 0.2 1.0
CB D:ASP120 4.6 0.7 1.0
CA D:GLY115 4.6 0.4 1.0
N D:ASN117 4.8 0.4 1.0
N D:ALA116 4.8 0.9 1.0
CB D:ASP114 4.8 0.6 1.0
CA D:ALA116 4.9 0.7 1.0
ND2 D:ASN117 5.0 0.6 1.0

Calcium binding site 8 out of 8 in 6bkj

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Calcium binding site 8 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Human Calpain-3 Protease Core in Complex with Leupeptin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:0.3
occ:1.00
 OD2 D:ASP371 2.4 0.3 1.0
O D:THR392 2.5 0.9 1.0
O D:GLU396 2.5 0.9 1.0
OD1 D:ASP394 2.7 0.4 1.0
OE2 D:GLU364 3.0 0.2 1.0
OD1 D:ASP371 3.1 0.5 1.0
CG D:ASP371 3.1 0.7 1.0
OE1 D:GLU364 3.2 0.9 1.0
CG D:ASP394 3.3 0.6 1.0
OD2 D:ASP394 3.3 0.3 1.0
CD D:GLU364 3.5 0.1 1.0
C D:THR392 3.6 0.8 1.0
C D:GLU396 3.6 0.5 1.0
CG2 D:THR392 3.9 0.5 1.0
O D:GLN390 4.0 0.1 1.0
N D:THR392 4.1 0.6 1.0
N D:ASP394 4.1 0.0 1.0
CA D:THR392 4.3 0.7 1.0
N D:GLU396 4.3 1.0 1.0
CA D:GLU396 4.4 0.2 1.0
CB D:ASP394 4.5 0.5 1.0
CB D:ASP371 4.6 0.0 1.0
N D:PHE397 4.6 0.8 1.0
CB D:THR392 4.7 0.7 1.0
N D:GLY395 4.7 0.1 1.0
N D:GLU393 4.7 0.2 1.0
CB D:GLU396 4.7 0.1 1.0
CA D:ASP394 4.8 0.9 1.0
CA D:PHE397 4.8 0.8 1.0
CG D:GLU364 4.9 0.8 1.0
CA D:GLU393 4.9 0.1 1.0

Reference:

Q.Ye, R.L.Campbell, P.L.Davies. Structures of Human Calpain-3 Protease Core with and Without Bound Inhibitor Reveal Mechanisms of Calpain Activation. J. Biol. Chem. V. 293 4056 2018.
ISSN: ESSN 1083-351X
PubMed: 29382717
DOI: 10.1074/JBC.RA117.001097
Page generated: Wed Jul 9 12:49:30 2025

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