Sodium in PDB 6bfo: Caspase-3 Mutant- T245D

All present enzymatic activity of Caspase-3 Mutant- T245D:
3.4.22.56;

The structure of Caspase-3 Mutant- T245D, PDB code: 6bfo 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)	35.59 / 1.54
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	68.264, 84.282, 96.000, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.4

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 11;

Binding sites:

The binding sites of Sodium atom in the Caspase-3 Mutant- T245D (pdb code 6bfo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 11 binding sites of Sodium where determined in the Caspase-3 Mutant- T245D, PDB code: 6bfo:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 11 in the Caspase-3 Mutant- T245D


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- T245D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:14.7 occ:1.00 OE1 A:GLN161 2.8 9.7 1.0 O B:TRP206 2.8 10.9 1.0 N B:PHE215 3.0 8.8 1.0 NE2 B:GLN261 3.0 9.8 1.0 CB B:PHE215 3.3 7.2 1.0 OG B:SER205 3.3 8.7 1.0 N B:TRP214 3.4 7.0 1.0 CD A:GLN161 3.5 8.6 1.0 NE2 A:GLN161 3.6 9.1 1.0 CB B:SER213 3.7 8.8 1.0 CA B:PHE215 3.7 8.6 1.0 CB B:TRP214 3.8 9.4 1.0 C B:TRP206 3.9 8.9 1.0 CD B:GLN261 3.9 8.9 1.0 C B:TRP214 3.9 8.1 1.0 CA B:TRP214 3.9 8.0 1.0 N B:TRP206 3.9 7.6 1.0 OE1 B:GLN261 4.0 12.0 1.0 C B:SER213 4.0 7.8 1.0 OG B:SER213 4.1 9.6 1.0 CB B:SER198 4.2 8.1 1.0 CA B:SER213 4.3 8.1 1.0 CA B:TRP206 4.4 9.3 1.0 CG B:TRP214 4.6 9.4 1.0 OG B:SER198 4.6 7.8 1.0 CG B:PHE215 4.6 7.2 1.0 CB B:SER205 4.7 8.0 1.0 C B:SER205 4.7 8.7 1.0 O B:SER198 4.8 8.3 1.0 N B:ILE216 4.8 7.8 1.0 C B:PHE215 4.8 6.6 1.0 CG A:GLN161 4.9 8.9 1.0 O B:SER213 4.9 8.4 1.0 CB B:TRP206 4.9 9.2 1.0 N B:ARG207 5.0 9.5 1.0

Sodium binding site 2 out of 11 in the Caspase-3 Mutant- T245D


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- T245D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na202 b:17.2 occ:1.00 OD2 A:ASP70 2.7 9.3 1.0 NH2 A:ARG64 2.9 9.3 1.0 OG1 A:THR67 2.9 9.7 1.0 CB A:THR67 3.5 9.9 1.0 CB A:LEU119 3.5 8.1 1.0 CG A:ASP70 3.6 9.8 1.0 CB A:ASP70 3.7 8.1 1.0 CA A:THR67 3.7 8.6 1.0 CZ A:ARG64 3.7 8.3 1.0 NH1 A:ARG64 3.7 9.0 1.0 CD2 A:LEU119 3.8 8.6 1.0 CG A:GLN161 3.8 8.9 1.0 CG A:LEU119 4.0 8.2 1.0 CD1 A:LEU119 4.0 10.0 1.0 O A:THR67 4.4 9.4 1.0 CA A:LEU119 4.4 7.7 1.0 OG B:SER213 4.5 9.6 1.0 CD B:ARG207 4.5 10.6 1.0 CB A:GLN161 4.6 8.3 1.0 C A:THR67 4.6 10.0 1.0 CB B:SER213 4.7 8.8 1.0 OD1 A:ASP70 4.7 9.3 1.0 N A:THR67 4.7 10.8 1.0 OD2 D:ASP5 4.9 20.3 1.0 C A:LEU119 5.0 9.1 1.0 CG2 A:THR67 5.0 8.8 1.0 NE A:ARG64 5.0 8.4 1.0

Sodium binding site 3 out of 11 in the Caspase-3 Mutant- T245D


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- T245D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na203 b:16.6 occ:1.00 O A:PHE143 2.9 11.2 1.0 O A:CYS148 3.0 11.9 1.0 NZ A:LYS156 3.0 8.6 1.0 C A:LEU151 3.2 9.9 1.0 N A:THR152 3.2 10.6 1.0 O A:LEU151 3.4 10.0 1.0 O A:ARG144 3.4 11.0 1.0 CE A:LYS156 3.5 8.7 1.0 CA A:GLY145 3.5 10.8 1.0 CB A:LEU151 3.5 9.2 1.0 CA A:THR152 3.6 10.0 1.0 CD A:LYS156 3.6 8.9 1.0 C A:ARG144 3.7 10.7 1.0 N A:GLY145 3.7 11.1 1.0 CA A:LEU151 3.9 10.9 1.0 C A:PHE143 3.9 9.2 1.0 C A:CYS148 4.0 12.4 1.0 OG1 A:THR152 4.1 11.3 1.0 CB A:CYS148 4.1 11.1 1.0 C A:GLY145 4.3 11.6 1.0 NA B:NA301 4.3 16.4 1.0 N A:LEU151 4.4 10.4 1.0 O A:GLY145 4.4 13.4 1.0 CB A:THR152 4.4 11.8 1.0 CA A:CYS148 4.5 12.5 1.0 N A:CYS148 4.6 12.6 1.0 CA A:ARG144 4.7 9.4 1.0 N A:ARG144 4.7 9.6 1.0 C A:THR152 4.8 10.7 1.0 CA A:PHE143 4.8 8.9 1.0 CG A:LYS156 4.8 8.3 1.0 SG A:CYS148 4.9 13.7 1.0 NA B:NA305 4.9 17.3 1.0 CG A:LEU151 5.0 9.1 1.0

Sodium binding site 4 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ A:Na204 b:17.3 occ:1.00 O A:ALA162 2.7 9.6 1.0 OG B:SER198 2.8 7.8 1.0 O A:ILE160 2.9 7.1 1.0 N B:SER198 3.2 8.1 1.0 N A:ALA162 3.7 7.6 1.0 CB B:SER198 3.7 8.1 1.0 N B:THR199 3.8 8.6 1.0 CG A:ARG164 3.8 9.1 1.0 C A:ALA162 3.8 8.9 1.0 CD A:ARG164 3.9 7.6 1.0 C A:ILE160 3.9 7.5 1.0 CA B:SER198 3.9 7.6 1.0 CG2 B:THR199 3.9 7.5 1.0 CB B:TYR197 4.0 6.9 1.0 C B:TYR197 4.0 8.6 1.0 CA B:TYR197 4.1 6.6 1.0 CD1 B:TYR197 4.1 10.5 1.0 CG2 A:ILE160 4.1 9.9 1.0 CA A:ALA162 4.3 7.8 1.0 C B:SER198 4.3 8.3 1.0 CB A:ILE160 4.4 9.2 1.0 CG B:TYR197 4.5 6.4 1.0 O B:THR199 4.6 8.0 1.0 CA A:GLN161 4.6 8.4 1.0 C A:GLN161 4.6 9.2 1.0 N A:GLN161 4.6 8.1 1.0 CB B:THR199 4.7 8.1 1.0 CB A:ALA162 4.7 9.7 1.0 CA B:THR199 4.7 7.7 1.0 CA A:ILE160 4.8 6.1 1.0 O A:HOH509 4.9 11.4 1.0 N A:CYS163 5.0 7.5 1.0 CB B:SER205 5.0 8.0 1.0

Sodium binding site 5 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:16.4 occ:1.00 OD2 B:ASP192 2.6 10.3 1.0 NA B:NA305 2.8 17.3 1.0 N A:GLY153 2.8 9.9 1.0 NZ A:LYS156 2.9 8.6 1.0 O B:ALA191 3.3 10.0 1.0 CB B:ASP192 3.4 8.7 1.0 CG B:ASP192 3.4 8.0 1.0 CD1 B:ILE187 3.5 19.6 1.0 CA A:GLY153 3.6 8.7 1.0 C A:THR152 3.8 10.7 1.0 CA A:THR152 3.8 10.0 1.0 CE A:LYS156 3.8 8.7 1.0 O A:LEU151 4.1 10.0 1.0 C B:ALA191 4.1 7.5 1.0 N A:LYS154 4.2 9.2 1.0 C A:GLY153 4.3 8.5 1.0 CG2 A:THR152 4.3 14.5 1.0 NA A:NA203 4.3 16.6 1.0 O A:LYS154 4.4 9.5 1.0 CA A:GLY145 4.5 10.8 1.0 CA B:ASP192 4.6 7.9 1.0 OD1 B:ASP192 4.6 8.0 1.0 N B:ASP192 4.7 7.1 1.0 CB A:THR152 4.7 11.8 1.0 O B:HOH428 4.7 14.3 1.0 N A:THR152 4.8 10.6 1.0 CG1 B:ILE187 4.8 15.9 1.0 C A:LEU151 4.9 9.9 1.0 CB B:ALA191 4.9 9.8 1.0 O A:THR152 4.9 11.8 1.0 N A:GLY145 5.0 11.1 1.0

Sodium binding site 6 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:15.6 occ:1.00 NA B:NA306 2.9 15.5 1.0 O B:TYR197 3.1 7.6 1.0 CA B:ALA196 3.2 7.4 1.0 C B:ALA196 3.4 7.5 1.0 N B:TYR197 3.4 7.6 1.0 O B:CYS264 3.4 8.1 1.0 CB B:ALA196 3.4 9.2 1.0 CE1 B:PHE215 3.6 7.6 1.0 C B:CYS264 3.7 6.3 1.0 CZ B:PHE215 3.7 8.9 1.0 CG1 B:ILE265 3.7 7.9 1.0 N B:ILE265 3.8 7.4 1.0 CA B:ILE265 3.9 6.5 1.0 C B:TYR197 3.9 8.6 1.0 N B:CYS264 4.0 6.6 1.0 O B:ALA196 4.1 8.6 1.0 CB B:PRO263 4.2 7.2 1.0 CA B:TYR197 4.3 6.6 1.0 CB B:ILE265 4.3 7.9 1.0 CA B:CYS264 4.5 7.6 1.0 CD2 B:LEU236 4.6 10.3 1.0 N B:ALA196 4.6 8.0 1.0 OD1 B:ASN240 4.6 9.6 1.0 O B:TYR195 4.7 10.0 1.0 C B:PRO263 4.8 9.1 1.0 CD1 B:PHE215 4.8 8.6 1.0 CD1 B:LEU236 4.8 10.0 1.0 CE2 B:PHE215 4.9 8.6 1.0 CD1 B:ILE265 5.0 10.1 1.0

Sodium binding site 7 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na303 b:16.6 occ:1.00 O B:VAL243 2.8 11.2 1.0 O B:PHE247 2.8 10.7 1.0 N B:GLN261 2.8 8.5 1.0 O B:GLN261 3.3 8.6 1.0 CE B:LYS260 3.3 10.8 1.0 CA B:LYS260 3.5 10.1 1.0 C B:LYS260 3.6 7.9 1.0 NZ B:LYS260 3.6 11.1 1.0 CB B:LYS260 3.7 10.0 1.0 O B:ALA244 3.7 12.6 1.0 C B:PHE247 3.8 9.0 1.0 CD B:LYS260 3.8 11.0 1.0 CA B:GLN261 3.8 8.3 1.0 C B:VAL243 3.8 9.7 1.0 CZ3 B:TRP214 3.9 10.7 1.0 CA B:ALA244 3.9 9.6 1.0 C B:GLN261 4.0 7.7 1.0 C B:ALA244 4.0 12.6 1.0 CB B:GLN261 4.2 9.1 1.0 CB B:PHE247 4.2 11.4 1.0 CE3 B:TRP214 4.2 9.1 1.0 N B:ALA244 4.3 8.1 1.0 CA B:PHE247 4.4 9.6 1.0 CG B:LYS260 4.4 11.2 1.0 N B:PHE247 4.5 11.3 1.0 CG1 B:VAL243 4.6 9.0 1.0 N B:GLU248 4.8 8.9 1.0 O B:LYS260 4.8 10.2 1.0 N B:LYS260 4.8 9.3 1.0 CH2 B:TRP214 4.8 8.9 1.0 O B:LYS259 4.9 9.7 1.0

Sodium binding site 8 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na304 b:15.8 occ:1.00 OG B:SER267 2.7 9.8 1.0 O B:HOH435 2.8 13.6 1.0 CG B:MET233 3.5 9.3 0.5 CG B:MET233 3.5 8.9 0.6 CB B:SER267 3.6 8.6 1.0 SD B:MET233 3.6 10.1 0.5 CB B:LEU269 3.7 10.2 1.0 SD B:MET233 3.7 9.6 0.6 CD1 B:LEU269 4.1 9.3 1.0 CE B:MET233 4.1 12.0 0.6 CG B:LEU269 4.2 7.6 1.0 CE B:MET233 4.4 14.0 0.5 O B:LEU269 4.5 10.5 1.0 CA B:LEU269 4.6 7.5 1.0 N B:LEU269 4.6 6.5 1.0 O B:LYS271 4.7 8.7 1.0 C B:LEU269 4.7 11.1 1.0 CB B:MET233 4.9 7.6 0.5 CB B:MET233 4.9 7.6 0.6 CA B:SER267 5.0 6.7 1.0

Sodium binding site 9 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na305 b:17.3 occ:1.00 NA B:NA301 2.8 16.4 1.0 O B:PRO188 2.8 12.3 1.0 O B:ALA191 2.9 10.0 1.0 O B:VAL189 3.1 11.4 1.0 CA A:GLY145 3.3 10.8 1.0 N A:GLY145 3.3 11.1 1.0 C B:VAL189 3.4 13.6 1.0 N B:ALA191 3.6 8.6 1.0 C B:ALA191 3.7 7.5 1.0 CA B:VAL189 3.7 9.4 1.0 CD1 B:ILE187 3.9 19.6 1.0 C B:PRO188 3.9 11.6 1.0 CA B:ALA191 4.0 8.1 1.0 CB B:ALA191 4.1 9.8 1.0 N B:GLU190 4.1 10.1 1.0 C B:GLU190 4.3 8.9 1.0 N B:VAL189 4.3 10.3 1.0 OD2 B:ASP192 4.4 10.3 1.0 NZ A:LYS156 4.5 8.6 1.0 C A:ARG144 4.5 10.7 1.0 CG1 B:ILE187 4.5 15.9 1.0 CE A:LYS156 4.6 8.7 1.0 CA B:GLU190 4.6 8.6 1.0 C A:GLY145 4.7 11.6 1.0 CE1 B:PHE193 4.7 10.6 1.0 N B:ASP192 4.9 7.1 1.0 NA A:NA203 4.9 16.6 1.0 CB B:ASP192 5.0 8.7 1.0

Sodium binding site 10 out of 11 in the Caspase-3 Mutant- T245D


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Caspase-3 Mutant- T245D within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:15.5 occ:1.00 OD1 B:ASN240 2.7 9.6 1.0 NA B:NA302 2.9 15.6 1.0 O B:LEU236 3.0 7.4 1.0 CG1 B:ILE265 3.7 7.9 1.0 CG B:ASN240 3.7 7.8 1.0 CG1 B:VAL239 3.7 8.7 1.0 CE1 B:PHE215 3.7 7.6 1.0 CB B:VAL239 3.7 7.8 1.0 CB B:PRO263 3.8 7.2 1.0 C B:LEU236 3.8 7.8 1.0 CB B:LEU236 3.9 6.7 1.0 N B:ASN240 3.9 8.2 1.0 CD2 B:LEU236 4.0 10.3 1.0 CA B:LEU236 4.0 7.2 1.0 CD1 B:ILE265 4.1 10.1 1.0 CG B:PRO263 4.3 7.2 1.0 C B:VAL239 4.4 8.7 1.0 ND2 B:ASN240 4.4 8.7 1.0 CA B:ASN240 4.5 8.0 1.0 CG B:LEU236 4.5 8.3 1.0 CB B:ASN240 4.6 7.7 1.0 CZ B:PHE215 4.6 8.9 1.0 CD1 B:PHE215 4.6 8.6 1.0 CA B:VAL239 4.6 8.8 1.0 CG2 B:VAL239 4.8 8.8 1.0 N B:CYS264 5.0 6.6 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