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Calcium in PDB 6bjd: Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64

Enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64

All present enzymatic activity of Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64:
3.4.22.54;

Protein crystallography data

The structure of Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64, PDB code: 6bjd 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) 17.93 / 2.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 60.280, 105.360, 225.360, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.4

Other elements in 6bjd:

The structure of Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64 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 in Complex with E- 64 (pdb code 6bjd). 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 E- 64, PDB code: 6bjd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Calcium binding site 1 out of 8 in 6bjd

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Calcium binding site 1 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca501

b:41.5
occ:1.00
 O A:ILE113 2.3 34.5 1.0
O A:GLY115 2.4 39.2 1.0
OE2 A:GLU199 2.4 33.1 1.0
OD2 A:ASP120 2.5 31.9 1.0
OD1 A:ASP120 2.8 40.1 1.0
ND2 A:ASN117 2.9 57.5 1.0
CG A:ASP120 2.9 36.2 1.0
OE1 A:GLU199 2.9 32.9 1.0
CD A:GLU199 3.1 32.0 1.0
C A:ILE113 3.5 33.4 1.0
C A:GLY115 3.6 37.9 1.0
O A:ASP114 3.8 41.3 1.0
C A:ASP114 4.0 41.2 1.0
CG A:ASN117 4.1 53.9 1.0
N A:ASN117 4.3 45.4 1.0
N A:GLY115 4.3 39.4 1.0
CB A:ASP120 4.4 37.6 1.0
N A:ILE113 4.4 32.1 1.0
N A:ASP114 4.4 38.3 1.0
CB A:ASP114 4.5 51.9 1.0
CA A:ASP114 4.5 42.7 1.0
CA A:ILE113 4.5 32.4 1.0
CA A:GLY115 4.5 39.7 1.0
N A:ALA116 4.5 38.9 1.0
CG A:GLU199 4.6 32.8 1.0
CA A:ALA116 4.6 39.2 1.0
CB A:ASN117 4.7 46.8 1.0
NE1 A:TRP201 4.7 30.6 1.0
CB A:ILE113 4.8 33.2 1.0
C A:ALA116 5.0 42.1 1.0
OD1 A:ASN117 5.0 58.1 1.0

Calcium binding site 2 out of 8 in 6bjd

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Calcium binding site 2 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca502

b:52.5
occ:1.00
 O A:GLU396 2.3 49.1 1.0
OD2 A:ASP371 2.4 86.0 1.0
OD1 A:ASP394 2.6 58.9 1.0
O A:THR392 2.6 71.6 1.0
OE2 A:GLU364 2.7 60.4 1.0
OE1 A:GLU364 2.7 64.1 1.0
OD1 A:ASP371 3.0 80.5 1.0
CG A:ASP371 3.1 78.2 1.0
CD A:GLU364 3.1 63.9 1.0
C A:GLU396 3.5 45.9 1.0
CG A:ASP394 3.6 57.6 1.0
C A:THR392 3.8 68.7 1.0
O A:GLN390 3.9 87.1 1.0
OD2 A:ASP394 4.0 59.6 1.0
N A:GLU396 4.1 46.1 1.0
CA A:GLU396 4.3 46.3 1.0
N A:ASP394 4.3 58.8 1.0
N A:THR392 4.3 72.8 1.0
CG2 A:THR392 4.5 68.6 1.0
N A:PHE397 4.5 45.7 1.0
CG A:GLU364 4.6 60.0 1.0
CB A:ASP371 4.6 77.6 1.0
CB A:GLU396 4.6 47.5 1.0
CA A:THR392 4.6 70.4 1.0
CA A:PHE397 4.7 45.9 1.0
N A:GLU393 4.8 67.7 1.0
CB A:ASP394 4.8 54.2 1.0
CA A:GLU393 4.9 67.8 1.0
N A:GLY395 4.9 42.3 1.0
CB A:PHE397 4.9 43.7 1.0
CA A:ASP394 5.0 53.8 1.0

Calcium binding site 3 out of 8 in 6bjd

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Calcium binding site 3 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca501

b:42.9
occ:1.00
 O B:ILE113 2.3 38.5 1.0
O B:GLY115 2.5 34.1 1.0
OE2 B:GLU199 2.5 41.7 1.0
OD2 B:ASP120 2.6 32.0 1.0
OD1 B:ASP120 2.8 39.0 1.0
OE1 B:GLU199 3.0 45.1 1.0
CG B:ASP120 3.0 34.6 1.0
OD1 B:ASN117 3.0 50.8 1.0
CD B:GLU199 3.1 42.7 1.0
C B:ILE113 3.5 35.8 1.0
C B:GLY115 3.7 40.0 1.0
O B:ASP114 3.8 49.1 1.0
C B:ASP114 3.9 45.8 1.0
CG B:ASN117 4.1 47.1 1.0
N B:GLY115 4.3 45.3 1.0
N B:ASP114 4.3 40.0 1.0
CB B:ASP114 4.4 50.5 1.0
CA B:ASP114 4.4 43.6 1.0
N B:ILE113 4.4 35.0 1.0
N B:ASN117 4.4 42.5 1.0
CA B:ILE113 4.4 34.2 1.0
CB B:ASP120 4.5 36.0 1.0
CA B:GLY115 4.5 43.0 1.0
CG B:GLU199 4.6 41.5 1.0
N B:ALA116 4.6 42.2 1.0
CA B:ALA116 4.7 45.1 1.0
CB B:ILE113 4.7 33.8 1.0
CB B:ASN117 4.8 42.1 1.0
NE1 B:TRP201 4.8 41.3 1.0

Calcium binding site 4 out of 8 in 6bjd

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Calcium binding site 4 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca502

b:54.8
occ:1.00
 O B:GLU396 2.3 55.0 1.0
OD2 B:ASP371 2.4 83.6 1.0
O B:THR392 2.5 64.7 1.0
OD1 B:ASP394 2.5 48.4 1.0
OE2 B:GLU364 2.6 45.4 1.0
OE1 B:GLU364 2.7 49.0 1.0
CD B:GLU364 3.0 51.3 1.0
OD1 B:ASP371 3.0 75.8 1.0
CG B:ASP371 3.1 78.1 1.0
C B:GLU396 3.5 48.6 1.0
CG B:ASP394 3.5 50.5 1.0
C B:THR392 3.7 65.9 1.0
OD2 B:ASP394 3.9 53.6 1.0
O B:GLN390 4.0 78.7 1.0
N B:GLU396 4.1 46.7 1.0
N B:ASP394 4.2 62.7 1.0
N B:THR392 4.3 67.1 1.0
CA B:GLU396 4.3 46.2 1.0
OG1 B:THR392 4.4 71.2 1.0
CG B:GLU364 4.5 54.4 1.0
N B:PHE397 4.5 49.1 1.0
CA B:THR392 4.6 68.1 1.0
CB B:ASP371 4.6 81.8 1.0
CB B:GLU396 4.6 46.0 1.0
N B:GLU393 4.7 66.7 1.0
CA B:PHE397 4.7 48.2 1.0
CB B:ASP394 4.7 53.8 1.0
CA B:GLU393 4.8 64.3 1.0
N B:GLY395 4.8 58.1 1.0
CA B:ASP394 4.9 58.2 1.0
CB B:PHE397 5.0 49.4 1.0

Calcium binding site 5 out of 8 in 6bjd

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Calcium binding site 5 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca501

b:37.7
occ:1.00
 OD2 C:ASP120 2.4 28.9 1.0
O C:ILE113 2.4 39.9 1.0
OE2 C:GLU199 2.4 31.8 1.0
O C:GLY115 2.5 39.6 1.0
OD1 C:ASP120 2.6 35.9 1.0
CG C:ASP120 2.9 32.6 1.0
OE1 C:GLU199 2.9 39.5 1.0
CD C:GLU199 3.0 35.1 1.0
ND2 C:ASN117 3.0 58.5 1.0
C C:ILE113 3.6 37.7 1.0
C C:GLY115 3.7 40.8 1.0
O C:ASP114 3.9 54.3 1.0
C C:ASP114 4.0 49.8 1.0
CG C:ASN117 4.1 55.6 1.0
CB C:ASP120 4.3 34.2 1.0
N C:ASN117 4.3 43.6 1.0
N C:GLY115 4.4 49.5 1.0
N C:ILE113 4.5 35.7 1.0
N C:ASP114 4.5 44.2 1.0
CB C:ASP114 4.5 52.0 1.0
CG C:GLU199 4.5 36.4 1.0
CA C:ASP114 4.5 46.6 1.0
CA C:ILE113 4.6 34.9 1.0
CA C:GLY115 4.6 45.9 1.0
N C:ALA116 4.6 40.1 1.0
CA C:ALA116 4.7 40.5 1.0
CB C:ASN117 4.7 46.2 1.0
NE1 C:TRP201 4.7 31.6 1.0
CB C:ILE113 4.8 33.0 1.0

Calcium binding site 6 out of 8 in 6bjd

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Calcium binding site 6 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:46.6
occ:1.00
 OD2 C:ASP371 2.3 54.6 1.0
O C:GLU396 2.4 33.7 1.0
O C:THR392 2.5 47.4 1.0
OD1 C:ASP394 2.6 46.6 1.0
OE2 C:GLU364 2.7 39.7 1.0
OE1 C:GLU364 2.7 45.0 1.0
OD1 C:ASP371 3.0 54.6 1.0
CG C:ASP371 3.0 51.8 1.0
CD C:GLU364 3.1 42.1 1.0
CG C:ASP394 3.5 45.7 1.0
C C:GLU396 3.6 35.1 1.0
C C:THR392 3.7 45.7 1.0
O C:GLN390 3.9 48.0 1.0
OD2 C:ASP394 3.9 51.3 1.0
N C:GLU396 4.2 35.9 1.0
N C:ASP394 4.2 49.6 1.0
N C:THR392 4.2 42.2 1.0
OG1 C:THR392 4.3 50.5 1.0
CA C:GLU396 4.4 36.2 1.0
CA C:THR392 4.5 45.0 1.0
CB C:ASP371 4.5 48.6 1.0
CG C:GLU364 4.5 42.2 1.0
N C:PHE397 4.6 35.8 1.0
N C:GLU393 4.7 48.7 1.0
CB C:GLU396 4.7 36.7 1.0
CB C:ASP394 4.7 45.6 1.0
CA C:GLU393 4.8 51.0 1.0
CA C:PHE397 4.8 37.3 1.0
N C:GLY395 4.9 41.7 1.0
CA C:ASP394 4.9 45.5 1.0
C C:GLN390 5.0 48.2 1.0

Calcium binding site 7 out of 8 in 6bjd

Go back to Calcium Binding Sites List in 6bjd
Calcium binding site 7 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca501

b:41.6
occ:1.00
 O D:ILE113 2.4 38.0 1.0
O D:GLY115 2.5 42.7 1.0
OE2 D:GLU199 2.5 36.4 1.0
OD2 D:ASP120 2.5 35.8 1.0
OD1 D:ASP120 2.7 46.5 1.0
ND2 D:ASN117 2.9 54.8 1.0
OE1 D:GLU199 2.9 36.6 1.0
CG D:ASP120 3.0 38.6 1.0
CD D:GLU199 3.1 37.3 1.0
C D:ILE113 3.6 38.1 1.0
C D:GLY115 3.7 43.0 1.0
O D:ASP114 3.8 50.9 1.0
C D:ASP114 4.0 46.4 1.0
CG D:ASN117 4.1 58.8 1.0
N D:GLY115 4.3 46.6 1.0
N D:ASN117 4.4 44.2 1.0
CB D:ASP120 4.4 37.2 1.0
N D:ASP114 4.4 42.8 1.0
CB D:ASP114 4.5 55.6 1.0
N D:ILE113 4.5 35.9 1.0
CA D:ASP114 4.5 46.3 1.0
CA D:ILE113 4.5 37.6 1.0
CG D:GLU199 4.6 36.5 1.0
CA D:GLY115 4.6 44.8 1.0
N D:ALA116 4.7 41.3 1.0
CB D:ASN117 4.7 52.1 1.0
CA D:ALA116 4.7 40.3 1.0
CB D:ILE113 4.8 39.8 1.0
NE1 D:TRP201 4.8 31.2 1.0

Calcium binding site 8 out of 8 in 6bjd

Go back to Calcium Binding Sites List in 6bjd
Calcium binding site 8 out of 8 in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64


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 E- 64 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca502

b:60.2
occ:1.00
 OD2 D:ASP371 2.3 90.6 1.0
O D:GLU396 2.4 54.8 1.0
O D:THR392 2.5 70.0 1.0
OD1 D:ASP394 2.6 66.3 1.0
OE2 D:GLU364 2.7 57.2 1.0
OE1 D:GLU364 2.8 54.8 1.0
OD1 D:ASP371 3.0 87.6 1.0
CG D:ASP371 3.0 90.8 1.0
CD D:GLU364 3.1 57.2 1.0
CG D:ASP394 3.5 66.0 1.0
C D:GLU396 3.6 52.1 1.0
C D:THR392 3.7 70.6 1.0
O D:GLN390 3.8 74.6 1.0
OD2 D:ASP394 3.9 66.2 1.0
N D:THR392 4.2 71.3 1.0
N D:GLU396 4.2 50.1 1.0
N D:ASP394 4.2 72.0 1.0
CG2 D:THR392 4.4 75.5 1.0
CA D:GLU396 4.4 51.2 1.0
CA D:THR392 4.5 70.9 1.0
CB D:ASP371 4.5 89.7 1.0
CG D:GLU364 4.6 55.9 1.0
N D:PHE397 4.6 50.4 1.0
N D:GLU393 4.7 72.4 1.0
CB D:GLU396 4.7 54.0 1.0
CB D:ASP394 4.8 65.0 1.0
CA D:GLU393 4.8 70.7 1.0
CA D:PHE397 4.8 50.6 1.0
N D:GLY395 4.9 58.1 1.0
CA D:ASP394 4.9 65.3 1.0
C D:GLN390 5.0 74.6 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: Mon Jul 15 17:01:31 2024

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