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

Go back to Calcium Binding Sites List in 6bjd
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

Go back to Calcium Binding Sites List in 6bjd
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

Go back to Calcium Binding Sites List in 6bjd
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

Go back to Calcium Binding Sites List in 6bjd
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

Go back to Calcium Binding Sites List in 6bjd
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

Go back to Calcium Binding Sites List in 6bjd
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: Sat Dec 12 05:58:51 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy