Chlorine in PDB 6bdt: 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;

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

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

Calcium

(Ca)

8 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S, PDB code: 6bdt:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl503 b:40.7 occ:1.00 N A:PHE155 3.3 39.2 1.0 N A:PHE111 3.3 34.7 1.0 O A:HOH631 3.3 43.6 1.0 OG A:SER154 3.5 44.9 1.0 CD A:ARG110 3.5 54.5 1.0 CA A:ARG110 3.6 37.8 1.0 CA A:SER154 3.8 42.0 1.0 C A:ARG110 4.0 37.6 1.0 C A:SER154 4.0 37.6 1.0 CB A:ARG110 4.1 45.8 1.0 CD2 A:PHE155 4.1 36.4 1.0 CB A:SER154 4.1 38.7 1.0 CB A:PHE111 4.2 34.5 1.0 CB A:PHE155 4.2 41.8 1.0 CA A:PHE155 4.2 43.7 1.0 O A:PRO109 4.3 40.5 1.0 CA A:PHE111 4.3 32.3 1.0 CG1 A:ILE156 4.4 54.7 1.0 N A:ILE156 4.4 51.4 1.0 CD2 B:HIS143 4.4 85.3 1.0 CG A:ARG110 4.5 49.8 1.0 NE A:ARG110 4.6 61.5 1.0 O A:GLN153 4.6 53.2 1.0 CG A:PHE155 4.6 38.8 1.0 N A:ARG110 4.7 38.4 1.0 C A:PHE155 4.8 46.1 1.0 CD1 A:ILE156 4.9 56.4 1.0 C A:PRO109 4.9 37.8 1.0 N A:SER154 5.0 40.5 1.0 NH1 A:ARG110 5.0 73.0 1.0 N A:ILE112 5.0 34.5 1.0

Chlorine binding site 2 out of 4 in the Crystal Structure of Human Calpain-3 Protease Core Mutant-C129S


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 Mutant-C129S within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl503 b:55.7 occ:1.00 N B:PHE111 3.2 42.2 1.0 N B:PHE155 3.3 55.1 1.0 OG B:SER154 3.4 65.1 1.0 CA B:ARG110 3.7 46.1 1.0 CD B:ARG110 3.7 61.8 1.0 CA B:SER154 3.7 59.2 1.0 C B:ARG110 4.0 45.0 1.0 CB B:SER154 4.0 61.2 1.0 C B:SER154 4.0 58.1 1.0 CB B:PHE111 4.1 35.7 1.0 CB B:ARG110 4.1 50.5 1.0 CD2 B:PHE155 4.1 65.5 1.0 CA B:PHE111 4.3 41.5 1.0 CB B:PHE155 4.3 61.5 1.0 CA B:PHE155 4.3 63.4 1.0 CG1 B:ILE156 4.4 67.3 1.0 N B:ILE156 4.4 60.6 1.0 O B:GLN153 4.4 62.3 1.0 O B:PRO109 4.5 52.4 1.0 CG B:ARG110 4.6 55.5 1.0 CD2 A:HIS143 4.7 58.4 1.0 CG B:PHE155 4.7 62.5 1.0 NE B:ARG110 4.7 66.5 1.0 N B:ARG110 4.8 50.1 1.0 N B:SER154 4.9 57.2 1.0 N B:ILE112 4.9 43.2 1.0 C B:PHE155 4.9 63.0 1.0 CD1 B:ILE156 5.0 64.4 1.0

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


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 Mutant-C129S within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl503 b:41.3 occ:1.00 N C:PHE111 3.3 32.7 1.0 N C:PHE155 3.4 35.0 1.0 CD C:ARG110 3.5 53.4 1.0 CA C:ARG110 3.5 38.2 1.0 OG C:SER154 3.6 48.6 1.0 CA C:SER154 3.9 37.8 1.0 C C:ARG110 3.9 34.2 1.0 CB C:ARG110 4.0 43.7 1.0 CD2 C:PHE155 4.1 38.8 1.0 C C:SER154 4.1 33.5 1.0 CB C:PHE111 4.2 31.6 1.0 CB C:SER154 4.2 39.0 1.0 CB C:PHE155 4.2 38.2 1.0 O C:PRO109 4.3 34.4 1.0 CA C:PHE155 4.3 40.0 1.0 CA C:PHE111 4.3 32.6 1.0 CG C:ARG110 4.4 46.0 1.0 N C:ILE156 4.4 47.4 1.0 CG1 C:ILE156 4.5 52.5 1.0 CD2 D:HIS143 4.5 58.4 1.0 NE C:ARG110 4.5 63.1 1.0 O C:GLN153 4.7 31.8 1.0 CD1 C:ILE156 4.7 52.3 1.0 N C:ARG110 4.7 39.2 1.0 CG C:PHE155 4.7 37.4 1.0 CG2 C:ILE156 4.8 51.4 1.0 C C:PHE155 4.9 45.2 1.0 C C:PRO109 4.9 36.1 1.0 N C:ILE112 4.9 33.8 1.0 O C:HOH623 4.9 43.7 1.0

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


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 Mutant-C129S within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl503 b:47.1 occ:1.00 N D:PHE111 3.2 32.5 1.0 N D:PHE155 3.4 44.7 1.0 OG D:SER154 3.5 48.9 1.0 CD D:ARG110 3.6 53.4 1.0 CA D:ARG110 3.6 41.2 1.0 CA D:SER154 3.8 46.8 1.0 C D:ARG110 3.9 35.2 1.0 CB D:ARG110 4.0 47.0 1.0 CB D:PHE111 4.1 34.3 1.0 C D:SER154 4.1 42.7 1.0 CD2 D:PHE155 4.1 52.2 1.0 CB D:SER154 4.1 49.2 1.0 CA D:PHE111 4.2 32.4 1.0 CB D:PHE155 4.3 45.7 1.0 CA D:PHE155 4.3 50.7 1.0 O D:PRO109 4.4 40.4 1.0 CG D:ARG110 4.5 51.0 1.0 CG1 D:ILE156 4.5 57.9 1.0 N D:ILE156 4.5 55.3 1.0 O D:GLN153 4.6 37.9 1.0 NE D:ARG110 4.6 56.1 1.0 CG D:PHE155 4.7 47.9 1.0 N D:ARG110 4.7 42.0 1.0 N D:ILE112 4.9 32.1 1.0 CB C:HIS143 4.9 43.4 1.0 N D:SER154 4.9 41.9 1.0 C D:PHE155 5.0 54.9 1.0 C D:PRO109 5.0 41.5 1.0

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