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Sodium in PDB 6bh9: Caspase-3 Mutant - T152A

Enzymatic activity of Caspase-3 Mutant - T152A

All present enzymatic activity of Caspase-3 Mutant - T152A:
3.4.22.56;

Protein crystallography data

The structure of Caspase-3 Mutant - T152A, PDB code: 6bh9 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) 35.61 / 1.94
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 108.362, 96.077, 68.212, 90.00, 128.96, 90.00
R / Rfree (%) 14.6 / 18.9

Other elements in 6bh9:

The structure of Caspase-3 Mutant - T152A also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Caspase-3 Mutant - T152A (pdb code 6bh9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Caspase-3 Mutant - T152A, PDB code: 6bh9:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6bh9

Go back to Sodium Binding Sites List in 6bh9
Sodium binding site 1 out of 5 in the Caspase-3 Mutant - T152A


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 - T152A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:16.0
occ:1.00
 OE1 A:GLN161 2.7 8.6 1.0
O C:TRP206 2.8 7.0 1.0
NE2 C:GLN261 2.9 13.3 1.0
N C:PHE215 3.0 7.8 1.0
OG C:SER205 3.2 9.1 1.0
CB C:PHE215 3.3 5.4 1.0
CD A:GLN161 3.4 8.5 1.0
N C:TRP214 3.4 7.5 1.0
NE2 A:GLN161 3.6 8.8 1.0
CB C:SER213 3.6 10.1 1.0
CA C:PHE215 3.7 7.4 1.0
CB C:TRP214 3.9 6.8 1.0
C C:TRP206 3.9 11.7 1.0
C C:TRP214 3.9 8.9 1.0
CD C:GLN261 3.9 11.2 1.0
CA C:TRP214 3.9 9.3 1.0
N C:TRP206 4.0 8.1 1.0
C C:SER213 4.0 10.7 1.0
OG C:SER213 4.1 7.4 1.0
CB C:SER198 4.1 6.6 1.0
OE1 C:GLN261 4.1 11.0 1.0
CA C:SER213 4.3 9.6 1.0
CA C:TRP206 4.5 10.1 1.0
OG C:SER198 4.5 10.0 1.0
CB C:SER205 4.6 6.4 1.0
CG C:TRP214 4.6 9.9 1.0
CG C:PHE215 4.6 7.6 1.0
C C:SER205 4.7 9.6 1.0
O C:SER198 4.7 5.9 1.0
N C:ILE216 4.8 6.8 1.0
CG A:GLN161 4.8 8.3 1.0
C C:PHE215 4.8 6.0 1.0
O C:SER213 4.9 10.2 1.0
CA C:SER205 5.0 10.3 1.0
N C:ARG207 5.0 12.7 1.0

Sodium binding site 2 out of 5 in 6bh9

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Sodium binding site 2 out of 5 in the Caspase-3 Mutant - T152A


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 - T152A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:17.2
occ:1.00
 OD2 A:ASP70 2.7 11.3 1.0
OG1 A:THR67 2.8 11.1 1.0
NH2 A:ARG64 2.9 12.2 1.0
CB A:THR67 3.5 14.1 1.0
CG A:ASP70 3.5 8.9 1.0
CB A:LEU119 3.5 5.4 1.0
CB A:ASP70 3.6 7.7 1.0
CA A:THR67 3.7 7.2 1.0
CZ A:ARG64 3.7 10.9 1.0
CG A:GLN161 3.7 8.3 1.0
NH1 A:ARG64 3.8 7.0 1.0
CD2 A:LEU119 3.9 7.0 1.0
CD1 A:LEU119 4.0 10.8 1.0
CG A:LEU119 4.0 6.2 1.0
O A:THR67 4.4 8.7 1.0
OG C:SER213 4.4 7.4 1.0
CA A:LEU119 4.4 8.7 1.0
C A:THR67 4.6 11.3 1.0
CB A:GLN161 4.6 8.4 1.0
CD C:ARG207 4.6 13.3 1.0
CB C:SER213 4.6 10.1 1.0
OD1 A:ASP70 4.7 5.6 1.0
N A:THR67 4.7 9.9 1.0
OD2 G:ASP5 4.9 20.3 1.0
CD A:GLN161 4.9 8.5 1.0
CG2 A:THR67 4.9 11.0 1.0
C A:LEU119 5.0 9.0 1.0

Sodium binding site 3 out of 5 in 6bh9

Go back to Sodium Binding Sites List in 6bh9
Sodium binding site 3 out of 5 in the Caspase-3 Mutant - T152A


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 - T152A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:19.1
occ:1.00
 OD2 C:ASP192 2.5 8.2 1.0
N A:GLY153 2.8 9.1 1.0
O C:HOH437 2.8 10.2 1.0
NZ A:LYS156 2.9 7.4 1.0
O C:ALA191 3.3 9.0 1.0
CG C:ASP192 3.3 10.9 1.0
CB C:ASP192 3.3 8.7 1.0
CA A:GLY153 3.6 9.6 1.0
CD1 C:ILE187 3.6 17.4 1.0
C A:ALA152 3.7 10.3 1.0
CA A:ALA152 3.7 7.8 1.0
CE A:LYS156 3.8 7.5 1.0
C C:ALA191 4.1 8.1 1.0
O A:LEU151 4.1 10.7 1.0
N A:LYS154 4.2 8.4 1.0
C A:GLY153 4.2 9.5 1.0
O A:HOH463 4.4 8.4 1.0
O A:LYS154 4.4 7.9 1.0
CA C:ASP192 4.5 9.6 1.0
OD1 C:ASP192 4.5 7.7 1.0
CB A:ALA152 4.6 11.0 1.0
O C:HOH418 4.6 13.6 1.0
N C:ASP192 4.6 9.3 1.0
CA A:GLY145 4.7 14.2 1.0
N A:ALA152 4.8 10.4 1.0
CB C:ALA191 4.8 8.2 1.0
C A:LEU151 4.9 9.4 1.0
O A:ALA152 4.9 12.2 1.0
CA C:ALA191 5.0 9.0 1.0

Sodium binding site 4 out of 5 in 6bh9

Go back to Sodium Binding Sites List in 6bh9
Sodium binding site 4 out of 5 in the Caspase-3 Mutant - T152A


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 - T152A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:15.6
occ:1.00
 OE1 B:GLN161 2.7 9.2 1.0
O E:TRP206 2.8 7.5 1.0
NE2 E:GLN261 2.9 14.6 1.0
N E:PHE215 3.0 9.4 1.0
OG E:SER205 3.1 11.7 1.0
CB E:PHE215 3.3 5.7 1.0
CD B:GLN161 3.4 9.2 1.0
N E:TRP214 3.5 7.8 1.0
NE2 B:GLN161 3.5 11.1 1.0
CB E:SER213 3.7 9.7 1.0
CA E:PHE215 3.8 6.5 1.0
C E:TRP206 3.9 10.2 1.0
CB E:TRP214 3.9 6.7 1.0
CD E:GLN261 3.9 13.6 1.0
N E:TRP206 3.9 7.2 1.0
C E:TRP214 4.0 8.2 1.0
CA E:TRP214 4.0 9.5 1.0
CB E:SER198 4.0 8.2 1.0
OG E:SER213 4.1 8.3 1.0
OE1 E:GLN261 4.1 10.8 1.0
C E:SER213 4.1 9.9 1.0
CA E:SER213 4.3 9.7 1.0
CA E:TRP206 4.4 9.6 1.0
CB E:SER205 4.5 6.7 1.0
OG E:SER198 4.5 9.7 1.0
CG E:PHE215 4.6 7.0 1.0
CG E:TRP214 4.7 9.1 1.0
O E:SER198 4.7 8.2 1.0
C E:SER205 4.7 11.1 1.0
CG B:GLN161 4.8 9.8 1.0
N E:ILE216 4.8 10.0 1.0
C E:PHE215 4.9 6.5 1.0
CA E:SER205 4.9 8.8 1.0
O E:SER213 4.9 9.8 1.0
CB E:TRP206 5.0 6.8 1.0
N E:ARG207 5.0 11.1 1.0

Sodium binding site 5 out of 5 in 6bh9

Go back to Sodium Binding Sites List in 6bh9
Sodium binding site 5 out of 5 in the Caspase-3 Mutant - T152A


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 - T152A within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:19.0
occ:1.00
 OD2 E:ASP192 2.6 10.2 1.0
O E:HOH433 2.8 11.2 1.0
N B:GLY153 2.8 11.7 1.0
NZ B:LYS156 2.9 9.4 1.0
O E:ALA191 3.3 8.7 1.0
CB E:ASP192 3.3 9.0 1.0
CG E:ASP192 3.3 11.9 1.0
CA B:GLY153 3.6 12.3 1.0
CD1 E:ILE187 3.7 15.3 1.0
C B:ALA152 3.7 9.6 1.0
CA B:ALA152 3.8 9.3 1.0
CE B:LYS156 3.8 7.8 1.0
C E:ALA191 4.0 9.6 1.0
O B:LEU151 4.1 10.8 1.0
N B:LYS154 4.2 8.4 1.0
C B:GLY153 4.2 11.3 1.0
O B:LYS154 4.3 6.8 1.0
O B:HOH461 4.4 8.1 1.0
CA E:ASP192 4.5 7.9 1.0
OD1 E:ASP192 4.6 9.0 1.0
N E:ASP192 4.6 8.3 1.0
CB B:ALA152 4.6 10.6 1.0
O E:HOH420 4.6 12.9 1.0
CA B:GLY145 4.7 11.2 1.0
CB E:ALA191 4.8 10.4 1.0
N B:ALA152 4.8 9.5 1.0
C B:LEU151 4.8 9.5 1.0
O B:ALA152 4.9 11.6 1.0
CA E:ALA191 4.9 7.3 1.0

Reference:

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
Page generated: Mon Aug 18 03:52:59 2025

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