Sodium in PDB 6bg0: Caspase-3 Mutant - D9A,D28A,S150D

All present enzymatic activity of Caspase-3 Mutant - D9A,D28A,S150D:
3.4.22.56;

The structure of Caspase-3 Mutant - D9A,D28A,S150D, PDB code: 6bg0 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)	35.66 / 2.13
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	108.872, 96.499, 68.914, 90.00, 126.71, 90.00
R / Rfree (%)	16.1 / 20.1

The binding sites of Sodium atom in the Caspase-3 Mutant - D9A,D28A,S150D (pdb code 6bg0). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Caspase-3 Mutant - D9A,D28A,S150D, PDB code: 6bg0:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Caspase-3 Mutant - D9A,D28A,S150D


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,S150D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:21.7 occ:1.00 O C:TRP206 2.7 12.2 1.0 OE1 A:GLN161 2.8 11.8 1.0 NE2 C:GLN261 2.9 12.5 1.0 N C:PHE215 3.0 10.1 1.0 CB C:PHE215 3.3 10.1 1.0 OG C:SER205 3.4 16.9 1.0 N C:TRP214 3.4 13.6 1.0 CD A:GLN161 3.5 14.1 1.0 NE2 A:GLN161 3.6 12.8 1.0 CB C:SER213 3.7 15.0 1.0 CA C:PHE215 3.7 15.7 1.0 C C:TRP206 3.8 15.3 1.0 CB C:TRP214 3.8 11.0 1.0 CD C:GLN261 3.8 13.9 1.0 N C:TRP206 3.9 13.3 1.0 C C:TRP214 3.9 15.1 1.0 CA C:TRP214 3.9 11.7 1.0 OE1 C:GLN261 4.0 18.0 1.0 C C:SER213 4.0 10.9 1.0 OG C:SER213 4.1 12.4 1.0 CB C:SER198 4.2 13.4 1.0 CA C:SER213 4.3 13.8 1.0 CA C:TRP206 4.3 15.1 1.0 CG C:TRP214 4.6 16.1 1.0 CB C:SER205 4.7 14.2 1.0 C C:SER205 4.7 17.4 1.0 CG C:PHE215 4.7 13.8 1.0 OG C:SER198 4.7 13.9 1.0 O C:SER198 4.8 14.2 1.0 CB C:TRP206 4.9 13.7 1.0 O C:SER213 4.9 15.9 1.0 N C:ARG207 4.9 17.7 1.0 C C:PHE215 4.9 12.6 1.0 N C:ILE216 4.9 12.2 1.0 CG A:GLN161 5.0 11.0 1.0 CA C:SER205 5.0 13.3 1.0

Sodium binding site 2 out of 2 in the Caspase-3 Mutant - D9A,D28A,S150D


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,S150D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:17.8 occ:1.00 OE1 B:GLN161 2.7 9.9 1.0 O D:TRP206 2.7 9.6 1.0 NE2 D:GLN261 2.9 10.1 1.0 N D:PHE215 3.0 11.3 1.0 OG D:SER205 3.2 15.8 1.0 CB D:PHE215 3.3 10.0 1.0 N D:TRP214 3.5 15.9 1.0 CD B:GLN161 3.5 14.5 1.0 CB D:SER213 3.7 15.9 1.0 NE2 B:GLN161 3.7 15.6 1.0 CA D:PHE215 3.8 14.8 1.0 CD D:GLN261 3.8 13.9 1.0 C D:TRP206 3.9 15.6 1.0 CB D:TRP214 3.9 14.1 1.0 OE1 D:GLN261 3.9 20.2 1.0 C D:TRP214 3.9 15.8 1.0 CA D:TRP214 3.9 11.1 1.0 N D:TRP206 4.0 12.9 1.0 OG D:SER213 4.1 12.9 1.0 C D:SER213 4.1 13.4 1.0 CB D:SER198 4.2 13.7 1.0 CA D:SER213 4.3 11.8 1.0 CA D:TRP206 4.4 13.4 1.0 OG D:SER198 4.5 12.6 1.0 CB D:SER205 4.5 12.1 1.0 CG D:TRP214 4.6 12.8 1.0 C D:SER205 4.7 17.6 1.0 CG D:PHE215 4.7 10.9 1.0 O D:SER198 4.8 10.9 1.0 N D:ILE216 4.9 10.3 1.0 C D:PHE215 4.9 12.0 1.0 CG B:GLN161 4.9 14.0 1.0 CA D:SER205 4.9 15.8 1.0 O D:SER213 4.9 15.0 1.0 CB D:TRP206 5.0 11.1 1.0 N D:ARG207 5.0 14.1 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