Atomistry » Sodium » PDB 6bg0-6c0l » 6bh9
Atomistry »
  Sodium »
    PDB 6bg0-6c0l »
      6bh9 »

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

Go back to Sodium Binding Sites List in 6bh9
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: Tue Oct 8 02:11:13 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy