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Calcium in PDB 6bgp: Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A

Enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A

All present enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A:
3.4.22.54;

Protein crystallography data

The structure of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A, PDB code: 6bgp 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) 17.94 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.100, 106.180, 225.620, 90.00, 90.00, 90.00
R / Rfree (%) 20.9 / 25.8

Other elements in 6bgp:

The structure of Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A 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-C129A (pdb code 6bgp). 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-C129A, PDB code: 6bgp:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6bgp

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:41.6
occ:1.00
 OD2 A:ASP120 2.3 34.0 1.0
O A:ILE113 2.3 42.2 1.0
OE2 A:GLU199 2.4 40.4 1.0
O A:GLY115 2.4 39.4 1.0
OD1 A:ASP120 2.8 41.4 1.0
OE1 A:GLU199 2.8 48.9 1.0
CG A:ASP120 2.9 38.2 1.0
CD A:GLU199 3.0 41.9 1.0
C A:ILE113 3.6 41.4 1.0
C A:GLY115 3.6 40.9 1.0
ND2 A:ASN117 3.8 68.1 1.0
C A:ASP114 4.2 48.9 1.0
N A:GLY115 4.3 48.1 1.0
CB A:ASP120 4.3 40.1 1.0
CG A:ASN117 4.3 61.6 1.0
N A:ILE113 4.3 40.6 1.0
O A:ASP114 4.3 48.9 1.0
OD1 A:ASN117 4.4 76.0 1.0
CA A:ILE113 4.4 38.6 1.0
N A:ASN117 4.4 43.9 1.0
CG A:GLU199 4.5 38.8 1.0
N A:ASP114 4.5 47.0 1.0
CB A:ASP114 4.5 57.3 1.0
N A:ALA116 4.5 42.7 1.0
CA A:GLY115 4.5 45.4 1.0
CA A:ALA116 4.6 41.9 1.0
CA A:ASP114 4.6 50.1 1.0
NE1 A:TRP201 4.7 33.1 1.0
CB A:ILE113 4.7 36.1 1.0
C A:ALA116 5.0 42.5 1.0

Calcium binding site 2 out of 8 in 6bgp

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:51.8
occ:1.00
 O A:GLU396 2.2 41.7 1.0
OD2 A:ASP371 2.3 66.6 1.0
OE2 A:GLU364 2.4 42.0 1.0
O A:THR392 2.5 47.8 1.0
OE1 A:GLU364 2.5 53.9 1.0
OD1 A:ASP394 2.7 47.0 1.0
CD A:GLU364 2.8 48.2 1.0
CG A:ASP371 3.1 65.3 1.0
OD1 A:ASP371 3.3 65.5 1.0
C A:GLU396 3.4 45.2 1.0
CG A:ASP394 3.6 48.1 1.0
C A:THR392 3.7 52.3 1.0
OD2 A:ASP394 4.0 51.2 1.0
N A:GLU396 4.1 42.6 1.0
O A:GLN390 4.1 55.0 1.0
N A:THR392 4.1 52.6 1.0
CA A:GLU396 4.2 43.8 1.0
OG1 A:THR392 4.2 61.6 1.0
CG A:GLU364 4.3 48.6 1.0
N A:ASP394 4.3 48.7 1.0
CA A:THR392 4.4 54.2 1.0
N A:PHE397 4.5 48.2 1.0
CB A:ASP371 4.5 66.5 1.0
CB A:GLU396 4.6 45.5 1.0
CA A:PHE397 4.7 47.3 1.0
N A:GLU393 4.7 52.8 1.0
CB A:ASP394 4.8 46.2 1.0
N A:GLY395 4.9 45.4 1.0
CB A:THR392 4.9 59.3 1.0
CA A:GLU393 4.9 55.1 1.0
CB A:PHE397 4.9 45.5 1.0

Calcium binding site 3 out of 8 in 6bgp

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:41.3
occ:1.00
 O B:ILE113 2.3 50.3 1.0
OD2 B:ASP120 2.4 38.6 1.0
OE2 B:GLU199 2.4 41.2 1.0
O B:GLY115 2.5 40.9 1.0
OD1 B:ASP120 2.8 45.1 1.0
OE1 B:GLU199 2.8 46.2 1.0
CG B:ASP120 2.9 39.7 1.0
CD B:GLU199 3.0 43.0 1.0
C B:ILE113 3.5 43.5 1.0
C B:GLY115 3.7 41.9 1.0
ND2 B:ASN117 3.8 58.9 1.0
C B:ASP114 4.1 50.5 1.0
N B:GLY115 4.3 50.5 1.0
O B:ASP114 4.3 50.9 1.0
CG B:ASN117 4.3 58.8 1.0
N B:ILE113 4.3 41.8 1.0
CB B:ASP120 4.4 40.7 1.0
OD1 B:ASN117 4.4 62.8 1.0
CA B:ILE113 4.4 40.9 1.0
N B:ASP114 4.4 47.8 1.0
CB B:ASP114 4.5 57.6 1.0
CG B:GLU199 4.5 42.3 1.0
N B:ASN117 4.5 46.5 1.0
CA B:ASP114 4.5 51.7 1.0
CA B:GLY115 4.6 47.0 1.0
N B:ALA116 4.6 41.5 1.0
CB B:ILE113 4.6 41.2 1.0
CA B:ALA116 4.7 45.7 1.0
NE1 B:TRP201 4.8 36.0 1.0

Calcium binding site 4 out of 8 in 6bgp

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:57.9
occ:1.00
 OD2 B:ASP371 2.2 81.6 1.0
O B:GLU396 2.3 42.2 1.0
O B:THR392 2.5 60.4 1.0
OE2 B:GLU364 2.5 48.0 1.0
OE1 B:GLU364 2.6 58.0 1.0
OD1 B:ASP394 2.7 45.6 1.0
CD B:GLU364 2.9 53.6 1.0
CG B:ASP371 3.1 81.1 1.0
OD1 B:ASP371 3.3 84.0 1.0
C B:GLU396 3.5 41.3 1.0
CG B:ASP394 3.6 45.4 1.0
C B:THR392 3.6 59.0 1.0
OD2 B:ASP394 4.0 50.3 1.0
N B:THR392 4.0 62.8 1.0
O B:GLN390 4.0 64.3 1.0
N B:GLU396 4.1 41.4 1.0
CA B:THR392 4.3 61.7 1.0
CA B:GLU396 4.3 41.9 1.0
N B:ASP394 4.3 54.2 1.0
CG B:GLU364 4.4 53.6 1.0
CB B:THR392 4.4 64.9 1.0
N B:PHE397 4.5 39.4 1.0
CB B:ASP371 4.5 82.3 1.0
CB B:GLU396 4.6 42.5 1.0
N B:GLU393 4.7 55.3 1.0
CA B:PHE397 4.7 40.6 1.0
CB B:ASP394 4.9 46.4 1.0
CA B:GLU393 4.9 58.2 1.0
N B:GLY395 5.0 49.8 1.0

Calcium binding site 5 out of 8 in 6bgp

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:42.0
occ:1.00
 O C:ILE113 2.3 44.3 1.0
OD2 C:ASP120 2.4 34.6 1.0
OE2 C:GLU199 2.4 41.4 1.0
O C:GLY115 2.4 44.0 1.0
OD1 C:ASP120 2.8 39.5 1.0
OE1 C:GLU199 2.8 43.3 1.0
CG C:ASP120 2.9 38.4 1.0
CD C:GLU199 3.0 44.6 1.0
C C:ILE113 3.5 42.4 1.0
C C:GLY115 3.7 39.5 1.0
ND2 C:ASN117 3.7 70.3 1.0
C C:ASP114 4.2 46.7 1.0
CG C:ASN117 4.3 62.1 1.0
N C:GLY115 4.3 42.0 1.0
O C:ASP114 4.3 50.1 1.0
OD1 C:ASN117 4.3 71.6 1.0
N C:ILE113 4.3 44.0 1.0
CB C:ASP120 4.4 40.0 1.0
CA C:ILE113 4.4 42.1 1.0
N C:ASN117 4.5 42.8 1.0
N C:ASP114 4.5 48.1 1.0
CB C:ASP114 4.5 55.9 1.0
CG C:GLU199 4.5 46.8 1.0
CA C:GLY115 4.6 40.4 1.0
N C:ALA116 4.6 38.0 1.0
CA C:ASP114 4.6 49.2 1.0
CA C:ALA116 4.6 36.6 1.0
CB C:ILE113 4.7 41.7 1.0
NE1 C:TRP201 4.8 37.8 1.0

Calcium binding site 6 out of 8 in 6bgp

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:72.5
occ:1.00
 OD2 C:ASP371 2.3 95.9 1.0
O C:THR392 2.4 66.1 1.0
O C:GLU396 2.5 61.4 1.0
OD1 C:ASP394 2.6 58.8 1.0
OE2 C:GLU364 2.7 59.1 1.0
OE1 C:GLU364 2.9 50.1 1.0
CD C:GLU364 3.1 52.7 1.0
CG C:ASP371 3.2 96.1 1.0
OD1 C:ASP371 3.4 87.7 1.0
CG C:ASP394 3.4 60.0 1.0
C C:THR392 3.5 71.3 1.0
C C:GLU396 3.6 62.5 1.0
OD2 C:ASP394 3.7 65.5 1.0
N C:THR392 3.9 81.0 1.0
O C:GLN390 3.9 90.6 1.0
CA C:THR392 4.1 75.7 1.0
N C:GLU396 4.2 57.9 1.0
CB C:THR392 4.2 78.8 1.0
N C:ASP394 4.3 63.8 1.0
CA C:GLU396 4.4 62.5 1.0
CB C:ASP371 4.6 99.7 1.0
CG C:GLU364 4.6 54.0 1.0
N C:GLU393 4.6 72.3 1.0
CB C:GLU396 4.7 67.0 1.0
N C:PHE397 4.7 59.9 1.0
CB C:ASP394 4.7 56.9 1.0
CA C:PHE397 4.9 56.8 1.0
CA C:GLU393 4.9 76.1 1.0
OG1 C:THR392 4.9 75.4 1.0
CA C:ASP394 5.0 57.1 1.0
C C:GLN390 5.0 89.7 1.0
N C:GLY395 5.0 54.4 1.0

Calcium binding site 7 out of 8 in 6bgp

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Calcium binding site 7 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:37.0
occ:1.00
 OD2 D:ASP120 2.3 36.8 1.0
O D:ILE113 2.3 40.0 1.0
O D:GLY115 2.4 38.6 1.0
OE2 D:GLU199 2.4 27.7 1.0
OD1 D:ASP120 2.8 45.1 1.0
OE1 D:GLU199 2.8 35.7 1.0
CG D:ASP120 2.9 39.3 1.0
CD D:GLU199 3.0 33.7 1.0
C D:ILE113 3.6 38.7 1.0
C D:GLY115 3.6 37.8 1.0
ND2 D:ASN117 3.7 55.9 1.0
C D:ASP114 4.2 46.7 1.0
CG D:ASN117 4.3 56.8 1.0
N D:GLY115 4.3 42.8 1.0
CB D:ASP120 4.3 39.0 1.0
O D:ASP114 4.3 47.2 1.0
OD1 D:ASN117 4.3 63.3 1.0
N D:ILE113 4.4 35.9 1.0
N D:ASN117 4.4 40.6 1.0
CA D:ILE113 4.4 36.2 1.0
N D:ASP114 4.5 43.2 1.0
CG D:GLU199 4.5 33.4 1.0
CB D:ASP114 4.5 54.4 1.0
N D:ALA116 4.5 38.3 1.0
CA D:GLY115 4.5 41.5 1.0
CA D:ALA116 4.5 39.1 1.0
CA D:ASP114 4.6 48.8 1.0
NE1 D:TRP201 4.7 33.1 1.0
CB D:ILE113 4.7 36.5 1.0
C D:ALA116 5.0 38.5 1.0

Calcium binding site 8 out of 8 in 6bgp

Go back to Calcium Binding Sites List in 6bgp
Calcium binding site 8 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129A


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-C129A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:54.5
occ:1.00
 OD2 D:ASP371 2.1 77.6 1.0
O D:THR392 2.3 63.0 1.0
O D:GLU396 2.4 48.1 1.0
OE2 D:GLU364 2.6 53.5 1.0
OD1 D:ASP394 2.7 56.6 1.0
OE1 D:GLU364 2.9 51.5 1.0
CG D:ASP371 3.1 77.5 1.0
CD D:GLU364 3.1 52.0 1.0
OD1 D:ASP371 3.3 70.8 1.0
C D:THR392 3.5 67.3 1.0
C D:GLU396 3.6 48.8 1.0
CG D:ASP394 3.6 57.8 1.0
N D:THR392 4.0 67.0 1.0
OD2 D:ASP394 4.0 53.8 1.0
O D:GLN390 4.1 77.5 1.0
N D:GLU396 4.2 46.9 1.0
N D:ASP394 4.2 64.2 1.0
CA D:THR392 4.2 67.4 1.0
CA D:GLU396 4.3 48.8 1.0
CB D:THR392 4.4 70.7 1.0
CB D:ASP371 4.5 76.6 1.0
N D:GLU393 4.6 66.4 1.0
CG D:GLU364 4.6 50.7 1.0
N D:PHE397 4.6 49.8 1.0
CA D:GLU393 4.7 66.7 1.0
CB D:GLU396 4.7 51.6 1.0
CB D:ASP394 4.8 56.9 1.0
CA D:PHE397 4.8 48.8 1.0
N D:GLY395 4.9 53.5 1.0
CA D:ASP394 4.9 56.8 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 12:47:57 2025

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