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Calcium in PDB 6bdt: Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S

Enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S

All present enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S:
3.4.22.54;

Protein crystallography data

The structure of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S, PDB code: 6bdt 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 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.810, 105.490, 225.260, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.6

Other elements in 6bdt:

The structure of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S (pdb code 6bdt). 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 Mutant-C129S, PDB code: 6bdt:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6bdt

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:33.4
occ:1.00
 O A:HOH623 2.3 35.2 1.0
O A:HOH602 2.3 30.0 1.0
O A:ILE113 2.3 43.6 1.0
OD2 A:ASP120 2.4 30.2 1.0
O A:GLY115 2.4 31.4 1.0
OE2 A:GLU199 2.4 35.7 1.0
OD1 A:ASP120 2.6 34.4 1.0
CG A:ASP120 2.8 30.6 1.0
OE1 A:GLU199 2.8 34.6 1.0
CD A:GLU199 3.0 33.1 1.0
C A:ILE113 3.5 39.3 1.0
C A:GLY115 3.6 34.0 1.0
C A:ASP114 4.2 38.4 1.0
N A:ILE113 4.2 34.3 1.0
CB A:ASP120 4.3 31.7 1.0
O A:ASP114 4.3 38.8 1.0
CA A:ILE113 4.3 38.1 1.0
N A:GLY115 4.4 38.6 1.0
ND2 A:ASN117 4.4 60.1 1.0
OD1 A:ASN117 4.4 59.6 1.0
N A:ASN117 4.5 40.1 1.0
CG A:GLU199 4.5 32.7 1.0
N A:ASP114 4.5 40.3 1.0
N A:ALA116 4.5 35.4 1.0
CA A:ALA116 4.6 35.8 1.0
CA A:GLY115 4.6 35.2 1.0
NE1 A:TRP201 4.6 29.9 1.0
CG A:ASN117 4.6 51.4 1.0
CB A:ILE113 4.6 35.1 1.0
CB A:ASP114 4.6 48.1 1.0
CA A:ASP114 4.6 42.0 1.0

Calcium binding site 2 out of 8 in 6bdt

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:51.7
occ:1.00
 O A:HOH630 2.0 45.0 1.0
OD2 A:ASP371 2.2 52.5 1.0
OE2 A:GLU364 2.3 48.0 1.0
O A:THR392 2.3 50.0 1.0
O A:GLU396 2.4 37.7 1.0
OE1 A:GLU364 2.5 56.2 1.0
OD1 A:ASP394 2.5 47.0 1.0
CD A:GLU364 2.7 49.0 1.0
CG A:ASP371 3.0 56.3 1.0
OD1 A:ASP371 3.2 58.5 1.0
C A:THR392 3.5 49.6 1.0
C A:GLU396 3.6 38.8 1.0
CG A:ASP394 3.6 45.5 1.0
N A:ASP394 4.0 45.2 1.0
N A:GLU396 4.0 35.6 1.0
OD2 A:ASP394 4.2 42.1 1.0
CG A:GLU364 4.3 48.2 1.0
N A:THR392 4.3 51.8 1.0
CA A:GLU396 4.3 37.6 1.0
O A:GLN390 4.4 49.8 1.0
N A:GLU393 4.4 49.3 1.0
O A:HOH601 4.4 41.1 1.0
CA A:THR392 4.5 54.4 1.0
CG2 A:THR392 4.5 62.8 1.0
CA A:GLU393 4.5 48.1 1.0
CB A:ASP371 4.5 56.0 1.0
N A:GLY395 4.5 37.8 1.0
N A:PHE397 4.6 42.4 1.0
CB A:ASP394 4.8 42.8 1.0
CA A:ASP394 4.8 43.2 1.0
C A:GLU393 4.8 46.8 1.0
CA A:PHE397 4.8 42.8 1.0
CB A:GLU396 4.9 37.4 1.0
CB A:PHE397 4.9 41.2 1.0
C A:GLY395 4.9 36.4 1.0
C A:ASP394 5.0 39.5 1.0

Calcium binding site 3 out of 8 in 6bdt

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:50.3
occ:1.00
 O B:HOH615 2.1 38.1 1.0
OE2 B:GLU364 2.2 49.5 1.0
O B:GLU396 2.3 44.8 1.0
OD2 B:ASP371 2.3 70.2 1.0
OE1 B:GLU364 2.4 58.5 1.0
O B:THR392 2.5 66.0 1.0
OD1 B:ASP394 2.5 44.3 1.0
CD B:GLU364 2.7 50.8 1.0
CG B:ASP371 3.1 67.5 1.0
OD1 B:ASP371 3.2 64.9 1.0
C B:GLU396 3.5 39.0 1.0
C B:THR392 3.7 57.6 1.0
CG B:ASP394 3.7 44.2 1.0
N B:GLU396 3.9 38.2 1.0
N B:ASP394 4.0 50.9 1.0
CG B:GLU364 4.2 50.1 1.0
CA B:GLU396 4.2 39.4 1.0
OD2 B:ASP394 4.2 44.4 1.0
O B:HOH613 4.4 48.5 1.0
N B:THR392 4.4 61.4 1.0
O B:GLN390 4.5 60.9 1.0
N B:GLY395 4.5 47.1 1.0
N B:PHE397 4.5 38.2 1.0
CA B:THR392 4.5 58.0 1.0
CB B:ASP371 4.5 71.6 1.0
N B:GLU393 4.6 54.1 1.0
CA B:GLU393 4.6 55.7 1.0
CA B:PHE397 4.7 38.6 1.0
CB B:PHE397 4.7 37.5 1.0
CB B:GLU396 4.8 37.9 1.0
CA B:ASP394 4.8 47.3 1.0
CB B:ASP394 4.8 44.3 1.0
C B:GLY395 4.8 43.1 1.0
CB B:THR392 4.8 61.0 1.0
C B:GLU393 4.9 55.8 1.0
C B:ASP394 5.0 50.1 1.0

Calcium binding site 4 out of 8 in 6bdt

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:35.1
occ:1.00
 O B:HOH605 2.1 39.2 1.0
O B:HOH612 2.2 40.8 1.0
OE2 B:GLU199 2.3 39.2 1.0
O B:ILE113 2.3 35.2 1.0
O B:GLY115 2.3 33.5 1.0
OD2 B:ASP120 2.4 29.9 1.0
OD1 B:ASP120 2.7 33.8 1.0
OE1 B:GLU199 2.8 33.7 1.0
CG B:ASP120 2.8 32.7 1.0
CD B:GLU199 2.9 38.2 1.0
C B:ILE113 3.5 36.3 1.0
C B:GLY115 3.6 38.6 1.0
N B:ILE113 4.2 35.7 1.0
C B:ASP114 4.2 43.6 1.0
N B:GLY115 4.3 42.3 1.0
CB B:ASP120 4.3 34.5 1.0
CA B:ILE113 4.3 38.3 1.0
O B:ASP114 4.3 42.0 1.0
CG B:GLU199 4.4 39.2 1.0
ND2 B:ASN117 4.4 57.9 1.0
OD1 B:ASN117 4.4 55.4 1.0
N B:ASP114 4.4 41.0 1.0
N B:ASN117 4.5 41.4 1.0
N B:ALA116 4.5 38.7 1.0
O B:HOH607 4.5 46.5 1.0
NE1 B:TRP201 4.5 35.4 1.0
CA B:GLY115 4.5 37.5 1.0
CA B:ALA116 4.5 40.6 1.0
CB B:ILE113 4.6 40.2 1.0
CG B:ASN117 4.6 53.2 1.0
CA B:ASP114 4.6 45.4 1.0
CB B:ASP114 4.7 49.6 1.0
CG2 B:ILE112 5.0 43.5 1.0

Calcium binding site 5 out of 8 in 6bdt

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:36.5
occ:1.00
 O C:HOH617 2.1 44.9 1.0
OE2 C:GLU199 2.3 35.7 1.0
O C:ILE113 2.3 34.0 1.0
OD2 C:ASP120 2.4 30.2 1.0
O C:GLY115 2.5 35.0 1.0
OD1 C:ASP120 2.6 32.4 1.0
OE1 C:GLU199 2.8 33.2 1.0
CG C:ASP120 2.8 31.3 1.0
CD C:GLU199 2.9 34.5 1.0
C C:ILE113 3.5 34.5 1.0
C C:GLY115 3.7 33.9 1.0
N C:ILE113 4.2 34.9 1.0
CB C:ASP120 4.3 35.9 1.0
CA C:ILE113 4.3 34.7 1.0
ND2 C:ASN117 4.3 65.0 1.0
C C:ASP114 4.3 37.6 1.0
CG C:GLU199 4.3 37.0 1.0
OD1 C:ASN117 4.4 67.2 1.0
N C:GLY115 4.4 33.5 1.0
O C:ASP114 4.4 41.0 1.0
N C:ASN117 4.5 44.6 1.0
CB C:ILE113 4.5 35.9 1.0
N C:ASP114 4.5 37.5 1.0
NE1 C:TRP201 4.6 33.9 1.0
N C:ALA116 4.6 35.7 1.0
CG C:ASN117 4.6 59.1 1.0
CA C:ALA116 4.6 40.1 1.0
CA C:GLY115 4.6 33.8 1.0
CB C:ASP114 4.7 46.8 1.0
CA C:ASP114 4.7 41.2 1.0

Calcium binding site 6 out of 8 in 6bdt

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:63.5
occ:1.00
 O C:THR392 2.3 62.3 1.0
OD2 C:ASP371 2.3 87.0 1.0
OD1 C:ASP394 2.4 45.9 1.0
O C:GLU396 2.5 57.9 1.0
OE2 C:GLU364 2.6 65.2 1.0
OE1 C:GLU364 2.9 57.0 1.0
CD C:GLU364 3.1 57.9 1.0
CG C:ASP371 3.1 77.7 1.0
OD1 C:ASP371 3.2 63.3 1.0
CG C:ASP394 3.5 52.5 1.0
C C:THR392 3.5 61.4 1.0
C C:GLU396 3.7 53.1 1.0
OD2 C:ASP394 4.0 56.6 1.0
N C:ASP394 4.0 55.0 1.0
N C:GLU396 4.1 44.7 1.0
N C:THR392 4.1 73.8 1.0
O C:GLN390 4.1 76.5 1.0
CG2 C:THR392 4.2 71.7 1.0
CA C:THR392 4.3 64.3 1.0
CA C:GLU396 4.3 51.8 1.0
N C:GLU393 4.5 61.2 1.0
CA C:GLU393 4.6 68.7 1.0
CB C:ASP371 4.6 77.3 1.0
CG C:GLU364 4.6 53.4 1.0
N C:GLY395 4.6 48.0 1.0
CB C:ASP394 4.7 48.3 1.0
N C:PHE397 4.7 50.7 1.0
CB C:GLU396 4.8 54.7 1.0
CA C:ASP394 4.8 48.9 1.0
CB C:THR392 4.8 68.5 1.0
C C:GLU393 4.8 64.5 1.0
CA C:PHE397 4.9 49.9 1.0

Calcium binding site 7 out of 8 in 6bdt

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Calcium binding site 7 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:53.4
occ:1.00
 OD2 D:ASP371 2.3 62.5 1.0
O D:GLU396 2.3 49.4 1.0
OE2 D:GLU364 2.4 49.2 1.0
O D:THR392 2.4 54.5 1.0
OD1 D:ASP394 2.5 45.4 1.0
OE1 D:GLU364 2.6 44.2 1.0
CD D:GLU364 2.9 49.3 1.0
CG D:ASP371 3.0 59.1 1.0
OD1 D:ASP371 3.1 50.4 1.0
C D:GLU396 3.5 44.2 1.0
CG D:ASP394 3.6 51.1 1.0
C D:THR392 3.7 62.1 1.0
N D:GLU396 4.0 40.1 1.0
N D:ASP394 4.1 59.5 1.0
OD2 D:ASP394 4.2 44.5 1.0
O D:GLN390 4.2 74.2 1.0
CA D:GLU396 4.2 42.4 1.0
N D:THR392 4.3 65.9 1.0
CG D:GLU364 4.4 50.6 1.0
CG2 D:THR392 4.5 69.0 1.0
CB D:ASP371 4.5 60.3 1.0
CA D:THR392 4.5 62.9 1.0
N D:PHE397 4.6 47.1 1.0
N D:GLY395 4.6 49.0 1.0
N D:GLU393 4.6 63.7 1.0
CA D:GLU393 4.7 63.0 1.0
CA D:PHE397 4.7 43.5 1.0
CB D:GLU396 4.8 47.3 1.0
CB D:ASP394 4.8 49.1 1.0
CB D:PHE397 4.8 44.3 1.0
CA D:ASP394 4.9 50.1 1.0
C D:GLY395 4.9 41.9 1.0
C D:GLU393 4.9 63.8 1.0

Calcium binding site 8 out of 8 in 6bdt

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Calcium binding site 8 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:32.8
occ:1.00
 O D:ILE113 2.3 32.2 1.0
OE2 D:GLU199 2.4 32.5 1.0
OD2 D:ASP120 2.5 32.9 1.0
O D:GLY115 2.5 34.9 1.0
OD1 D:ASP120 2.6 32.9 1.0
OE1 D:GLU199 2.8 34.6 1.0
CG D:ASP120 2.8 32.0 1.0
CD D:GLU199 2.9 34.0 1.0
C D:ILE113 3.5 34.4 1.0
C D:GLY115 3.7 35.1 1.0
C D:ASP114 4.2 40.6 1.0
N D:ILE113 4.3 32.9 1.0
CB D:ASP120 4.3 34.3 1.0
CA D:ILE113 4.3 32.2 1.0
N D:GLY115 4.4 38.1 1.0
O D:ASP114 4.4 43.8 1.0
OD1 D:ASN117 4.4 56.5 1.0
ND2 D:ASN117 4.4 52.5 1.0
CG D:GLU199 4.4 34.6 1.0
N D:ASP114 4.5 40.9 1.0
N D:ASN117 4.5 38.7 1.0
CB D:ILE113 4.6 32.4 1.0
CG D:ASN117 4.6 49.9 1.0
N D:ALA116 4.6 37.7 1.0
CA D:GLY115 4.6 35.6 1.0
NE1 D:TRP201 4.6 34.2 1.0
CA D:ALA116 4.7 36.4 1.0
CB D:ASP114 4.7 53.8 1.0
CA D:ASP114 4.7 45.5 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 12:44:40 2025

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