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Chlorine 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:

Calcium (Ca) 8 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Calpain-3 Protease Core in Complex with E- 64, PDB code: 6bjd:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 6bjd

Go back to Chlorine Binding Sites List in 6bjd
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl503

b:41.8
occ:1.00
 N A:PHE111 3.2 31.9 1.0
OG A:SER154 3.2 51.9 1.0
N A:PHE155 3.3 40.1 1.0
CD A:ARG110 3.5 49.1 1.0
CA A:ARG110 3.5 38.9 1.0
CA A:SER154 3.7 46.2 1.0
C A:ARG110 3.9 35.8 1.0
CB A:ARG110 4.0 41.2 1.0
CB A:SER154 4.0 45.5 1.0
CD2 A:PHE155 4.0 34.8 1.0
C A:SER154 4.1 41.3 1.0
CB A:PHE155 4.2 38.6 1.0
CB A:PHE111 4.2 31.7 1.0
CA A:PHE155 4.2 41.1 1.0
N A:ILE156 4.3 50.2 1.0
CA A:PHE111 4.3 31.2 1.0
CG A:ARG110 4.3 44.0 1.0
O A:PRO109 4.3 36.0 1.0
CG1 A:ILE156 4.6 47.8 1.0
CG A:PHE155 4.6 35.6 1.0
CG2 A:ILE156 4.6 48.9 1.0
NE A:ARG110 4.6 57.5 1.0
O A:GLN153 4.6 46.7 1.0
N A:ARG110 4.7 37.5 1.0
C A:PHE155 4.8 45.7 1.0
C A:PRO109 4.9 37.6 1.0
CD1 A:ILE156 4.9 50.8 1.0
N A:SER154 5.0 49.1 1.0

Chlorine binding site 2 out of 4 in 6bjd

Go back to Chlorine Binding Sites List in 6bjd
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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
B:Cl503

b:54.0
occ:1.00
 CD B:ARG110 3.2 53.5 1.0
N B:PHE111 3.3 41.9 1.0
OG B:SER154 3.3 54.1 1.0
CA B:ARG110 3.4 45.5 1.0
N B:PHE155 3.5 57.5 1.0
CA B:SER154 3.9 52.6 1.0
C B:ARG110 3.9 42.3 1.0
CB B:ARG110 3.9 46.5 1.0
CB B:SER154 4.1 53.0 1.0
CD2 B:PHE155 4.1 65.3 1.0
CG B:ARG110 4.2 48.7 1.0
C B:SER154 4.2 54.2 1.0
CB B:PHE155 4.2 56.3 1.0
NE B:ARG110 4.2 60.0 1.0
CB B:PHE111 4.3 40.6 1.0
O B:PRO109 4.3 45.6 1.0
N B:ILE156 4.3 54.4 1.0
CA B:PHE155 4.4 57.2 1.0
CA B:PHE111 4.4 40.3 1.0
CG1 B:ILE156 4.5 64.5 1.0
CG2 B:ILE156 4.5 67.5 1.0
N B:ARG110 4.6 45.3 1.0
CG B:PHE155 4.7 60.0 1.0
O B:GLN153 4.8 52.8 1.0
O B:HOH613 4.8 40.0 1.0
CD1 B:ILE156 4.8 65.9 1.0
C B:PHE155 4.8 53.5 1.0
NH1 B:ARG110 4.9 67.5 1.0
C B:PRO109 4.9 45.8 1.0
CZ B:ARG110 4.9 60.9 1.0
N B:ILE112 5.0 37.6 1.0

Chlorine binding site 3 out of 4 in 6bjd

Go back to Chlorine Binding Sites List in 6bjd
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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
C:Cl503

b:39.7
occ:1.00
 OG C:SER154 3.1 38.2 1.0
N C:PHE155 3.3 43.2 1.0
N C:PHE111 3.3 34.8 1.0
CD C:ARG110 3.5 42.9 1.0
CA C:SER154 3.6 43.4 1.0
CA C:ARG110 3.7 36.5 1.0
CB C:SER154 3.8 42.0 1.0
C C:SER154 4.0 41.4 1.0
C C:ARG110 4.0 35.9 1.0
CD2 C:PHE155 4.1 40.9 1.0
CB C:PHE111 4.1 37.0 1.0
CB C:ARG110 4.1 38.4 1.0
CB C:PHE155 4.3 38.6 1.0
CA C:PHE155 4.3 42.1 1.0
N C:ILE156 4.3 45.5 1.0
CA C:PHE111 4.3 34.0 1.0
O C:GLN153 4.5 46.6 1.0
CG C:ARG110 4.5 40.5 1.0
NE C:ARG110 4.5 48.2 1.0
O C:PRO109 4.5 37.2 1.0
CG1 C:ILE156 4.6 52.7 1.0
CG C:PHE155 4.7 37.8 1.0
CG2 C:ILE156 4.7 53.3 1.0
N C:SER154 4.8 43.9 1.0
C C:PHE155 4.8 43.7 1.0
N C:ARG110 4.8 34.6 1.0
N C:ILE112 5.0 33.2 1.0
CD1 C:ILE156 5.0 52.7 1.0

Chlorine binding site 4 out of 4 in 6bjd

Go back to Chlorine Binding Sites List in 6bjd
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl 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
D:Cl503

b:41.0
occ:1.00
 OG D:SER154 3.1 46.6 1.0
N D:PHE111 3.2 35.5 1.0
N D:PHE155 3.4 50.7 1.0
CA D:SER154 3.6 48.0 1.0
CD D:ARG110 3.6 52.8 1.0
CA D:ARG110 3.7 40.9 1.0
CB D:SER154 3.8 47.1 1.0
C D:ARG110 3.9 37.8 1.0
CB D:PHE111 4.0 32.3 1.0
C D:SER154 4.0 48.4 1.0
CD2 D:PHE155 4.1 52.6 1.0
CB D:ARG110 4.1 43.1 1.0
CA D:PHE111 4.2 33.8 1.0
CB D:PHE155 4.3 53.2 1.0
CA D:PHE155 4.4 52.5 1.0
N D:ILE156 4.4 56.8 1.0
O D:GLN153 4.4 49.4 1.0
CG D:ARG110 4.5 45.2 1.0
O D:PRO109 4.6 40.7 1.0
CG1 D:ILE156 4.7 58.3 1.0
CG D:PHE155 4.7 53.3 1.0
NE D:ARG110 4.7 60.3 1.0
N D:SER154 4.8 47.6 1.0
CG2 D:ILE156 4.8 63.5 1.0
N D:ARG110 4.8 40.5 1.0
N D:ILE112 4.9 33.9 1.0
C D:PHE155 4.9 54.8 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: Fri Jul 26 22:51:01 2024

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