Sodium in PDB 6bgk: Caspase-3 Mutant- D9A,D28A,T152D

All present enzymatic activity of Caspase-3 Mutant- D9A,D28A,T152D:
3.4.22.56;

The structure of Caspase-3 Mutant- D9A,D28A,T152D, PDB code: 6bgk was solved by M.E.Thomas, R.Grinshpon, P.D.Swartz, A.C.Clark, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.76 / 1.87
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.054, 69.133, 84.638, 90.00, 131.37, 90.00
R / Rfree (%)	15.9 / 21.1

The structure of Caspase-3 Mutant- D9A,D28A,T152D also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Caspase-3 Mutant- D9A,D28A,T152D (pdb code 6bgk). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Caspase-3 Mutant- D9A,D28A,T152D, PDB code: 6bgk:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Caspase-3 Mutant- D9A,D28A,T152D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Caspase-3 Mutant- D9A,D28A,T152D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:13.7 occ:1.00 O B:PHE143 2.9 13.0 1.0 O B:CYS148 2.9 9.8 1.0 NZ B:LYS156 3.0 5.8 1.0 C B:LEU151 3.4 7.5 1.0 CE B:LYS156 3.4 8.6 1.0 O B:LEU151 3.4 8.6 1.0 CB B:LEU151 3.5 5.7 1.0 O B:ARG144 3.5 11.6 1.0 CD B:LYS156 3.6 8.8 1.0 OD1 B:ASP152 3.6 12.3 1.0 CA B:GLY145 3.6 8.5 1.0 N B:ASP152 3.7 11.2 1.0 C B:ARG144 3.8 9.3 1.0 N B:GLY145 3.8 12.5 1.0 CA B:LEU151 3.9 11.1 1.0 C B:PHE143 4.0 6.6 1.0 C B:CYS148 4.0 15.5 1.0 CB B:CYS148 4.1 13.1 1.0 CA B:ASP152 4.1 8.6 1.0 CL D:CL301 4.3 25.9 1.0 N B:LEU151 4.4 11.5 1.0 C B:GLY145 4.5 11.9 1.0 CA B:CYS148 4.5 12.4 1.0 O B:GLY145 4.5 11.6 1.0 CG B:ASP152 4.7 15.0 1.0 N B:CYS148 4.7 8.8 1.0 SG B:CYS148 4.7 13.0 1.0 O D:HOH446 4.7 8.8 1.0 CG B:LYS156 4.7 8.6 1.0 CA B:ARG144 4.8 7.2 1.0 CA B:PHE143 4.8 11.9 1.0 N B:ARG144 4.8 6.5 1.0 CG B:LEU151 4.8 6.8 1.0

Sodium binding site 2 out of 3 in the Caspase-3 Mutant- D9A,D28A,T152D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Caspase-3 Mutant- D9A,D28A,T152D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na203 b:14.4 occ:1.00 NH2 B:ARG64 2.7 7.8 1.0 OG1 B:THR67 2.8 10.8 1.0 OD2 B:ASP70 2.8 11.6 1.0 CB B:LEU119 3.5 5.7 1.0 CB B:THR67 3.5 10.7 1.0 CZ B:ARG64 3.6 14.1 1.0 CG B:ASP70 3.7 7.2 1.0 CG B:GLN161 3.7 8.9 1.0 NH1 B:ARG64 3.7 5.8 1.0 CA B:THR67 3.7 5.8 1.0 CB B:ASP70 3.8 5.5 1.0 CD2 B:LEU119 3.8 6.8 1.0 CG B:LEU119 3.9 6.6 1.0 CD1 B:LEU119 4.0 8.5 1.0 CA B:LEU119 4.4 10.1 1.0 O B:THR67 4.4 7.5 1.0 CB B:GLN161 4.5 7.8 1.0 CD D:ARG207 4.6 7.9 1.0 OG D:SER213 4.6 8.7 1.0 C B:THR67 4.6 9.1 1.0 CB D:SER213 4.6 10.8 1.0 N B:THR67 4.8 8.7 1.0 OD1 B:ASP70 4.8 6.7 1.0 OD2 H:ASP5 4.9 20.3 1.0 NE B:ARG64 4.9 8.3 1.0 C B:LEU119 4.9 7.3 1.0 CD B:GLN161 4.9 7.7 1.0 CG2 B:THR67 4.9 10.2 1.0

Sodium binding site 3 out of 3 in the Caspase-3 Mutant- D9A,D28A,T152D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Caspase-3 Mutant- D9A,D28A,T152D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na204 b:15.5 occ:1.00 O D:TRP206 2.8 7.2 1.0 OE1 B:GLN161 2.8 9.7 1.0 N D:PHE215 2.9 7.5 1.0 NE2 D:GLN261 2.9 9.2 1.0 OG D:SER205 3.2 9.5 1.0 CB D:PHE215 3.3 7.5 1.0 N D:TRP214 3.4 8.4 1.0 CD B:GLN161 3.5 7.7 1.0 NE2 B:GLN161 3.6 7.5 1.0 CA D:PHE215 3.7 8.5 1.0 CB D:SER213 3.7 10.8 1.0 CB D:TRP214 3.8 8.5 1.0 CD D:GLN261 3.9 10.8 1.0 C D:TRP206 3.9 8.3 1.0 C D:TRP214 3.9 8.6 1.0 CA D:TRP214 3.9 7.6 1.0 N D:TRP206 3.9 6.7 1.0 OE1 D:GLN261 3.9 12.7 1.0 C D:SER213 4.1 11.7 1.0 OG D:SER213 4.1 8.7 1.0 CB D:SER198 4.1 4.9 1.0 CA D:SER213 4.3 13.2 1.0 CA D:TRP206 4.4 8.2 1.0 CB D:SER205 4.6 7.6 1.0 OG D:SER198 4.6 8.1 1.0 CG D:TRP214 4.6 5.5 1.0 C D:SER205 4.7 10.7 1.0 CG D:PHE215 4.7 5.7 1.0 O D:SER198 4.7 5.2 1.0 N D:ILE216 4.8 9.2 1.0 C D:PHE215 4.8 9.1 1.0 O D:SER213 4.9 8.3 1.0 CG B:GLN161 4.9 8.9 1.0 CA D:SER205 4.9 6.7 1.0 N D:ARG207 5.0 7.2 1.0 CB D:TRP206 5.0 4.1 1.0

M.E.Thomas, R.Grinshpon, P.Swartz, A.C.Clark. Modifications to A Common Phosphorylation Network Provide Individualized Control in Caspases. J. Biol. Chem. V. 293 5447 2018.
ISSN: ESSN 1083-351X
PubMed: 29414778
DOI: 10.1074/JBC.RA117.000728