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Sodium in PDB 6bfk: Caspase-3 Mutant- T245A

Enzymatic activity of Caspase-3 Mutant- T245A

All present enzymatic activity of Caspase-3 Mutant- T245A:
3.4.22.56;

Protein crystallography data

The structure of Caspase-3 Mutant- T245A, PDB code: 6bfk 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) 36.04 / 1.75
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 128.724, 68.996, 85.384, 90.00, 131.16, 90.00
R / Rfree (%) 15.3 / 18

Sodium Binding Sites:

The binding sites of Sodium atom in the Caspase-3 Mutant- T245A (pdb code 6bfk). 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- T245A, PDB code: 6bfk:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in 6bfk

Go back to Sodium Binding Sites List in 6bfk
Sodium binding site 1 out of 5 in the Caspase-3 Mutant- T245A


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- T245A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na201

b:23.0
occ:1.00
 OE1 A:GLN161 2.7 18.1 1.0
O C:TRP206 2.8 17.9 1.0
N C:PHE215 3.0 14.6 1.0
NE2 C:GLN261 3.0 18.1 1.0
CB C:PHE215 3.3 13.7 1.0
OG C:SER205 3.4 17.2 1.0
CD A:GLN161 3.5 19.4 1.0
N C:TRP214 3.5 15.4 1.0
NE2 A:GLN161 3.6 16.3 1.0
CB C:SER213 3.7 19.7 1.0
CA C:PHE215 3.7 15.6 1.0
CB C:TRP214 3.9 17.0 1.0
CD C:GLN261 3.9 17.2 1.0
C C:TRP214 3.9 15.0 1.0
C C:TRP206 3.9 17.5 1.0
CA C:TRP214 4.0 17.0 1.0
OE1 C:GLN261 4.0 20.3 1.0
N C:TRP206 4.0 18.1 1.0
OG C:SER213 4.1 18.6 1.0
C C:SER213 4.1 17.8 1.0
CB C:SER198 4.2 13.7 1.0
CA C:SER213 4.4 18.4 1.0
CA C:TRP206 4.5 15.0 1.0
CG C:PHE215 4.6 14.8 1.0
OG C:SER198 4.7 17.4 1.0
CG C:TRP214 4.7 16.1 1.0
CB C:SER205 4.7 17.1 1.0
C C:SER205 4.8 18.1 1.0
N C:ILE216 4.8 17.7 1.0
CG A:GLN161 4.8 15.6 1.0
C C:PHE215 4.8 15.5 1.0
O C:SER198 4.9 15.3 1.0
O C:SER213 4.9 18.6 1.0

Sodium binding site 2 out of 5 in 6bfk

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Sodium binding site 2 out of 5 in the Caspase-3 Mutant- T245A


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- T245A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:25.2
occ:1.00
 O A:ALA162 2.7 15.6 1.0
OG C:SER198 2.8 17.4 1.0
O A:ILE160 2.9 14.5 1.0
N C:SER198 3.2 14.7 1.0
N A:ALA162 3.7 14.7 1.0
CB C:SER198 3.8 13.7 1.0
N C:THR199 3.8 14.4 1.0
C A:ALA162 3.8 17.4 1.0
CG A:ARG164 3.8 17.7 1.0
C A:ILE160 3.9 15.9 1.0
CA C:SER198 3.9 14.8 1.0
CD A:ARG164 3.9 14.9 1.0
CG2 C:THR199 4.0 14.0 1.0
CB C:TYR197 4.1 15.0 1.0
C C:TYR197 4.1 16.8 1.0
CD1 C:TYR197 4.1 17.7 1.0
CG2 A:ILE160 4.1 17.0 1.0
CA C:TYR197 4.1 16.6 1.0
C C:SER198 4.3 15.0 1.0
CA A:ALA162 4.3 18.9 1.0
CB A:ILE160 4.4 18.6 1.0
CA A:GLN161 4.6 17.0 1.0
C A:GLN161 4.6 16.7 1.0
CG C:TYR197 4.6 16.0 1.0
O C:THR199 4.6 15.0 1.0
N A:GLN161 4.6 15.9 1.0
CB C:THR199 4.7 15.0 1.0
CA C:THR199 4.7 13.8 1.0
CB A:ALA162 4.7 17.4 1.0
CA A:ILE160 4.8 15.1 1.0
N A:CYS163 5.0 15.8 1.0
O A:HOH449 5.0 18.9 1.0

Sodium binding site 3 out of 5 in 6bfk

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Sodium binding site 3 out of 5 in the Caspase-3 Mutant- T245A


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- T245A within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na301

b:25.9
occ:1.00
 OD2 C:ASP192 2.7 19.0 1.0
O C:HOH439 2.7 18.8 1.0
N A:GLY153 2.8 17.8 1.0
NZ A:LYS156 3.0 18.7 1.0
CD1 C:ILE187 3.1 26.9 0.4
O C:ALA191 3.4 19.4 1.0
CB C:ASP192 3.4 15.9 1.0
CG C:ASP192 3.5 18.5 1.0
CA A:GLY153 3.7 17.9 1.0
C A:THR152 3.8 19.7 1.0
CA A:THR152 3.8 17.3 1.0
CE A:LYS156 3.8 19.5 1.0
C C:ALA191 4.1 17.4 1.0
O A:LEU151 4.2 18.4 1.0
CG2 A:THR152 4.2 22.9 1.0
N A:LYS154 4.3 17.2 1.0
C A:GLY153 4.4 17.5 1.0
CG2 C:ILE187 4.4 29.8 0.6
O A:HOH487 4.4 19.1 1.0
CA A:GLY145 4.5 21.3 1.0
CG1 C:ILE187 4.5 27.8 0.4
O A:LYS154 4.5 17.5 1.0
CA C:ASP192 4.6 16.9 1.0
CB A:THR152 4.6 21.7 1.0
OD1 C:ASP192 4.7 19.4 1.0
N C:ASP192 4.7 16.9 1.0
O C:HOH424 4.7 22.6 1.0
N A:THR152 4.8 20.4 1.0
CB C:ALA191 4.8 18.7 1.0
C A:LEU151 4.9 17.8 1.0
O A:THR152 4.9 19.8 1.0

Sodium binding site 4 out of 5 in 6bfk

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Sodium binding site 4 out of 5 in the Caspase-3 Mutant- T245A


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- T245A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na301

b:23.4
occ:1.00
 OE1 B:GLN161 2.7 18.4 1.0
O D:TRP206 2.9 17.1 1.0
N D:PHE215 3.0 15.8 1.0
NE2 D:GLN261 3.0 19.3 1.0
CB D:PHE215 3.3 14.2 1.0
OG D:SER205 3.4 17.7 1.0
CD B:GLN161 3.5 18.3 1.0
N D:TRP214 3.5 16.2 1.0
NE2 B:GLN161 3.6 16.5 1.0
CB D:SER213 3.7 19.6 1.0
CA D:PHE215 3.7 14.6 1.0
CB D:TRP214 3.9 16.6 1.0
C D:TRP214 3.9 18.5 1.0
CD D:GLN261 3.9 17.4 1.0
CA D:TRP214 4.0 16.7 1.0
OE1 D:GLN261 4.0 20.3 1.0
C D:TRP206 4.0 17.7 1.0
N D:TRP206 4.1 15.6 1.0
OG D:SER213 4.1 16.4 1.0
C D:SER213 4.1 17.1 1.0
CB D:SER198 4.2 14.5 1.0
CA D:SER213 4.4 14.6 1.0
CA D:TRP206 4.5 15.0 1.0
OG D:SER198 4.6 16.4 1.0
CG D:PHE215 4.6 14.9 1.0
CG D:TRP214 4.7 18.5 1.0
CB D:SER205 4.7 18.5 1.0
O D:SER198 4.8 14.9 1.0
N D:ILE216 4.8 17.2 1.0
CG B:GLN161 4.8 16.9 1.0
C D:PHE215 4.8 18.3 1.0
C D:SER205 4.9 17.6 1.0
O D:SER213 4.9 17.6 1.0

Sodium binding site 5 out of 5 in 6bfk

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Sodium binding site 5 out of 5 in the Caspase-3 Mutant- T245A


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- T245A within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na301

b:25.4
occ:1.00
 OD2 D:ASP192 2.6 19.1 1.0
O D:HOH434 2.8 19.2 1.0
N B:GLY153 2.8 17.4 1.0
NZ B:LYS156 3.0 19.4 1.0
O D:ALA191 3.4 19.7 1.0
CD1 D:ILE187 3.4 31.7 1.0
CB D:ASP192 3.4 18.3 1.0
CG D:ASP192 3.4 19.1 1.0
CA B:GLY153 3.6 16.3 1.0
C B:THR152 3.7 20.2 1.0
CA B:THR152 3.8 16.7 1.0
CE B:LYS156 3.8 19.4 1.0
O B:LEU151 4.1 17.4 1.0
C D:ALA191 4.2 19.2 1.0
CG2 B:THR152 4.2 22.1 1.0
N B:LYS154 4.3 16.8 1.0
C B:GLY153 4.3 17.9 1.0
O B:HOH512 4.4 18.5 1.0
O B:LYS154 4.5 17.4 1.0
CA B:GLY145 4.5 21.9 1.0
CA D:ASP192 4.6 17.3 1.0
CB B:THR152 4.6 24.8 1.0
OD1 D:ASP192 4.7 17.4 1.0
N D:ASP192 4.7 15.4 1.0
O D:HOH428 4.7 23.0 1.0
CG1 D:ILE187 4.7 28.6 1.0
N B:THR152 4.8 20.6 1.0
C B:LEU151 4.9 18.0 1.0
CB D:ALA191 4.9 21.3 1.0
O B:THR152 4.9 20.3 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 02:04:27 2024

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