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Sodium in PDB 6bg4: Caspase-3 Mutant- T152D

Enzymatic activity of Caspase-3 Mutant- T152D

All present enzymatic activity of Caspase-3 Mutant- T152D:
3.4.22.56;

Protein crystallography data

The structure of Caspase-3 Mutant- T152D, PDB code: 6bg4 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) 36.31 / 1.87
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 109.209, 96.685, 68.626, 90.00, 126.76, 90.00
R / Rfree (%) 16.4 / 20.7

Other elements in 6bg4:

The structure of Caspase-3 Mutant- T152D also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Sodium atom in the Caspase-3 Mutant- T152D (pdb code 6bg4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 13 binding sites of Sodium where determined in the Caspase-3 Mutant- T152D, PDB code: 6bg4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 13 in 6bg4

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Sodium binding site 1 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na301

b:18.8
occ:1.00
O E:TRP206 2.8 12.1 1.0
OE1 A:GLN161 2.8 11.1 1.0
N E:PHE215 2.9 8.4 1.0
NE2 E:GLN261 3.0 11.8 1.0
CB E:PHE215 3.2 10.0 1.0
OG E:SER205 3.3 11.7 1.0
N E:TRP214 3.4 12.6 1.0
CD A:GLN161 3.5 13.8 1.0
NE2 A:GLN161 3.5 12.4 1.0
CB E:SER213 3.7 14.3 1.0
CA E:PHE215 3.7 11.3 1.0
CB E:TRP214 3.7 9.2 1.0
C E:TRP214 3.8 12.0 1.0
CA E:TRP214 3.9 10.5 1.0
C E:TRP206 3.9 11.6 1.0
CD E:GLN261 3.9 11.7 1.0
N E:TRP206 3.9 10.7 1.0
OE1 E:GLN261 4.0 14.5 1.0
OG E:SER213 4.0 11.2 1.0
C E:SER213 4.0 11.8 1.0
CB E:SER198 4.2 11.6 1.0
CA E:SER213 4.3 13.4 1.0
CA E:TRP206 4.4 9.7 1.0
CG E:TRP214 4.5 13.3 1.0
OG E:SER198 4.6 12.9 1.0
CG E:PHE215 4.6 11.2 1.0
CB E:SER205 4.6 10.3 1.0
C E:SER205 4.7 11.8 1.0
C E:PHE215 4.8 13.8 1.0
N E:ILE216 4.8 11.9 1.0
O E:SER198 4.8 10.9 1.0
CG A:GLN161 4.9 10.1 1.0
O E:SER213 4.9 13.7 1.0
CB E:TRP206 5.0 9.7 1.0
N E:ARG207 5.0 11.1 1.0

Sodium binding site 2 out of 13 in 6bg4

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Sodium binding site 2 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:22.1
occ:1.00
OE2 A:GLU124 2.5 18.1 1.0
O A:HOH516 2.7 26.4 1.0
O A:HOH520 2.8 18.5 1.0
O E:HOH403 2.8 20.1 1.0
CD A:GLU124 3.5 16.9 1.0
CA A:GLY125 3.6 12.1 1.0
N A:GLY125 3.6 14.5 1.0
O A:HOH480 3.8 21.0 1.0
CG A:GLU124 3.9 13.8 1.0
O B:HOH393 4.0 23.2 1.0
O A:HOH525 4.1 23.5 1.0
O A:HOH459 4.1 12.3 1.0
NH2 A:ARG164 4.1 11.1 1.0
O A:HOH504 4.2 18.7 1.0
O B:HOH414 4.4 26.0 1.0
C A:GLU124 4.4 15.6 1.0
OE1 A:GLU124 4.6 21.8 1.0
OH E:TYR197 4.7 18.7 1.0
O E:HOH456 4.8 15.8 1.0
C A:GLY125 5.0 13.0 1.0

Sodium binding site 3 out of 13 in 6bg4

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Sodium binding site 3 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na301

b:18.0
occ:1.00
O E:HOH418 2.6 16.8 1.0
O E:LYS260 2.6 13.3 1.0
N A:ASP169 3.0 13.5 1.0
NE1 E:TRP206 3.1 13.4 1.0
CB E:LYS259 3.6 11.3 1.0
CA A:LEU168 3.7 13.4 1.0
C E:LYS260 3.7 8.6 1.0
CD2 A:LEU168 3.8 14.9 1.0
O A:ASP169 3.8 14.2 1.0
C A:LEU168 3.8 12.4 1.0
CB A:ASP169 3.8 13.6 1.0
CD1 E:TRP206 3.9 10.5 1.0
CA A:ASP169 3.9 12.6 1.0
N E:LYS260 3.9 10.4 1.0
CB A:LEU168 4.1 16.1 1.0
CE2 E:TRP206 4.2 10.7 1.0
C A:ASP169 4.3 15.8 1.0
C E:LYS259 4.4 13.2 1.0
CA E:LYS260 4.5 12.5 1.0
CG E:LYS259 4.6 12.0 1.0
CA E:LYS259 4.6 13.6 1.0
CG A:LEU168 4.6 16.1 1.0
CZ2 E:TRP206 4.7 11.2 1.0
O A:GLU167 4.8 11.7 1.0
N E:GLN261 4.8 10.3 1.0
O E:TYR204 5.0 14.0 1.0
CA E:GLN261 5.0 11.2 1.0
N A:LEU168 5.0 15.2 1.0

Sodium binding site 4 out of 13 in 6bg4

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Sodium binding site 4 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na302

b:18.4
occ:1.00
OD1 E:ASN240 2.7 12.3 1.0
O E:HOH444 2.9 12.9 1.0
O E:LEU236 3.0 12.4 1.0
CG E:ASN240 3.6 11.4 1.0
CG1 E:ILE265 3.7 10.3 1.0
CB E:PRO263 3.7 8.8 1.0
CB E:VAL239 3.8 11.8 1.0
CG1 E:VAL239 3.8 7.4 1.0
CE1 E:PHE215 3.8 12.2 1.0
C E:LEU236 3.8 13.2 1.0
CB E:LEU236 3.9 13.3 1.0
N E:ASN240 4.0 11.2 1.0
CD2 E:LEU236 4.0 13.4 1.0
CA E:LEU236 4.0 10.9 1.0
CD1 E:ILE265 4.1 10.1 1.0
CG E:PRO263 4.2 11.4 1.0
ND2 E:ASN240 4.4 10.8 1.0
CG E:LEU236 4.5 13.9 1.0
CA E:ASN240 4.5 9.9 1.0
C E:VAL239 4.5 12.8 1.0
CB E:ASN240 4.6 10.4 1.0
CZ E:PHE215 4.6 11.3 1.0
CD1 E:PHE215 4.7 12.0 1.0
CA E:VAL239 4.7 10.1 1.0
CG2 E:VAL239 4.8 12.6 1.0
N E:THR237 5.0 11.8 1.0
CA E:PRO263 5.0 9.4 1.0

Sodium binding site 5 out of 13 in 6bg4

Go back to Sodium Binding Sites List in 6bg4
Sodium binding site 5 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na303

b:19.9
occ:1.00
O A:HOH444 2.6 14.2 1.0
OG1 E:THR199 2.8 11.4 1.0
N E:ILE262 3.0 9.5 1.0
O E:HOH418 3.1 16.8 1.0
CA E:GLN261 3.4 11.2 1.0
O E:ILE262 3.5 11.4 1.0
CG E:GLN261 3.6 11.9 1.0
C E:GLN261 3.7 13.3 1.0
CB E:GLN261 3.9 9.2 1.0
N E:ALA200 3.9 11.8 1.0
CB E:TYR203 4.0 13.0 1.0
CB E:THR199 4.1 10.8 1.0
CA E:ILE262 4.1 10.0 1.0
CG E:TYR203 4.2 14.2 1.0
CG2 E:ILE262 4.2 12.1 1.0
C E:ILE262 4.2 11.3 1.0
O E:LYS260 4.2 13.3 1.0
O E:TYR204 4.3 14.0 1.0
CD2 E:TYR203 4.3 13.6 1.0
CA E:THR199 4.4 10.1 1.0
CB E:ALA200 4.4 13.5 1.0
N E:GLN261 4.5 10.3 1.0
CB A:ASP169 4.6 13.6 1.0
OD2 A:ASP169 4.6 14.8 1.0
CB E:ILE262 4.7 10.4 1.0
C E:THR199 4.7 14.4 1.0
CD E:GLN261 4.8 11.7 1.0
C E:LYS260 4.8 8.6 1.0
CA E:ALA200 4.8 12.6 1.0
CD1 E:TYR203 4.8 12.9 1.0
O E:GLN261 4.9 11.1 1.0

Sodium binding site 6 out of 13 in 6bg4

Go back to Sodium Binding Sites List in 6bg4
Sodium binding site 6 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na201

b:18.7
occ:1.00
O F:TRP206 2.7 11.8 1.0
OE1 B:GLN161 2.8 12.3 1.0
N F:PHE215 2.9 10.8 1.0
NE2 F:GLN261 3.0 13.8 1.0
CB F:PHE215 3.3 9.3 1.0
OG F:SER205 3.3 11.5 1.0
N F:TRP214 3.4 10.2 1.0
CD B:GLN161 3.5 11.7 1.0
NE2 B:GLN161 3.5 11.8 1.0
CB F:SER213 3.6 14.7 1.0
CA F:PHE215 3.7 11.7 1.0
CB F:TRP214 3.8 7.4 1.0
C F:TRP206 3.8 11.8 1.0
C F:TRP214 3.9 16.5 1.0
CA F:TRP214 3.9 12.0 1.0
CD F:GLN261 3.9 12.6 1.0
N F:TRP206 3.9 8.7 1.0
OE1 F:GLN261 4.0 13.6 1.0
C F:SER213 4.0 13.0 1.0
OG F:SER213 4.1 11.7 1.0
CB F:SER198 4.2 10.6 1.0
CA F:SER213 4.2 10.5 1.0
CA F:TRP206 4.4 10.0 1.0
OG F:SER198 4.6 11.0 1.0
CB F:SER205 4.6 10.0 1.0
CG F:TRP214 4.6 14.5 1.0
CG F:PHE215 4.6 11.0 1.0
C F:SER205 4.7 11.1 1.0
N F:ILE216 4.8 10.8 1.0
O F:SER213 4.8 14.3 1.0
C F:PHE215 4.8 12.9 1.0
O F:SER198 4.8 12.0 1.0
CG B:GLN161 4.9 10.0 1.0
CB F:TRP206 4.9 8.3 1.0
N F:ARG207 4.9 13.0 1.0

Sodium binding site 7 out of 13 in 6bg4

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Sodium binding site 7 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na202

b:20.6
occ:1.00
OG1 B:THR67 2.7 12.5 1.0
NH2 B:ARG64 2.7 10.0 1.0
OD2 B:ASP70 2.8 17.5 1.0
CB B:THR67 3.4 13.2 1.0
CB B:LEU119 3.5 12.9 1.0
CA B:THR67 3.6 15.3 1.0
CZ B:ARG64 3.6 12.3 1.0
CG B:ASP70 3.7 13.5 1.0
NH1 B:ARG64 3.7 13.7 1.0
CD2 B:LEU119 3.8 10.8 1.0
CB B:ASP70 3.8 11.3 1.0
CG B:GLN161 3.8 10.0 1.0
CD1 B:LEU119 3.9 14.4 1.0
CG B:LEU119 3.9 10.9 1.0
O B:THR67 4.3 13.3 1.0
CA B:LEU119 4.4 11.4 1.0
C B:THR67 4.5 17.4 1.0
OG F:SER213 4.5 11.7 1.0
CD F:ARG207 4.5 12.7 1.0
CB B:GLN161 4.5 11.1 1.0
N B:THR67 4.6 12.8 1.0
CB F:SER213 4.7 14.7 1.0
OD1 B:ASP70 4.8 12.4 1.0
CG2 B:THR67 4.8 15.2 1.0
NE B:ARG64 4.9 12.7 1.0
C B:LEU119 4.9 12.7 1.0
OD2 D:ASP5 4.9 20.3 1.0

Sodium binding site 8 out of 13 in 6bg4

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Sodium binding site 8 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na203

b:24.1
occ:1.00
O F:HOH430 2.6 13.9 1.0
OD2 B:ASP169 2.8 14.5 1.0
CG E:GLU190 3.4 15.6 1.0
CD2 F:TYR203 3.4 11.8 1.0
CE2 F:TYR203 3.5 12.0 1.0
CB E:GLU190 3.5 11.5 1.0
CG F:TYR203 3.5 10.9 1.0
CG B:ASP169 3.6 15.3 1.0
CB B:ASP169 3.6 13.1 1.0
CZ F:TYR203 3.7 14.2 1.0
CD1 F:TYR203 3.7 14.9 1.0
CG2 F:ILE262 3.7 9.2 1.0
CB F:ALA200 3.8 12.5 1.0
CE1 F:TYR203 3.8 15.3 1.0
CB F:TYR203 4.3 11.4 1.0
N F:ILE262 4.3 12.6 1.0
OH F:TYR203 4.4 15.3 1.0
O F:HOH421 4.6 18.2 1.0
CD E:GLU190 4.7 23.7 1.0
CA E:GLU190 4.8 12.8 1.0
N E:GLU190 4.8 16.1 1.0
CA B:ASP169 4.8 14.5 1.0
OD1 B:ASP169 4.8 15.8 1.0
N F:ALA200 4.8 10.3 1.0
CB F:ILE262 4.8 8.6 1.0
O F:ILE262 4.9 9.6 1.0
CB E:PRO188 4.9 10.7 1.0
CA F:ALA200 4.9 12.0 1.0
OG1 F:THR199 5.0 11.7 1.0
CA F:GLN261 5.0 11.9 1.0

Sodium binding site 9 out of 13 in 6bg4

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Sodium binding site 9 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na301

b:21.8
occ:1.00
O F:HOH425 2.7 15.0 1.0
OD2 F:ASP192 2.8 15.9 1.0
NZ B:LYS156 2.8 13.2 1.0
N B:GLY153 2.8 11.3 1.0
O F:ALA191 3.4 15.4 1.0
CD1 F:ILE187 3.5 20.0 1.0
CB F:ASP192 3.5 14.0 1.0
CG F:ASP192 3.5 13.2 1.0
CA B:GLY153 3.6 12.5 1.0
C B:ASP152 3.7 14.6 1.0
CA B:ASP152 3.7 15.5 1.0
CE B:LYS156 3.8 12.1 1.0
O B:LEU151 3.9 12.6 1.0
N B:LYS154 4.2 15.1 1.0
C F:ALA191 4.2 14.7 1.0
C B:GLY153 4.3 13.0 1.0
O B:HOH366 4.3 13.7 1.0
O B:LYS154 4.4 12.3 1.0
OD1 B:ASP152 4.6 20.3 1.0
N B:ASP152 4.6 15.0 1.0
C B:LEU151 4.6 16.4 1.0
O F:HOH413 4.7 18.7 1.0
CA F:ASP192 4.7 14.0 1.0
CB B:ASP152 4.7 18.2 1.0
OD1 F:ASP192 4.7 13.6 1.0
CA B:GLY145 4.8 14.6 1.0
N F:ASP192 4.8 13.9 1.0
CG1 F:ILE187 4.8 17.0 1.0
O B:ASP152 4.9 18.2 1.0
CB F:ALA191 4.9 11.9 1.0

Sodium binding site 10 out of 13 in 6bg4

Go back to Sodium Binding Sites List in 6bg4
Sodium binding site 10 out of 13 in the Caspase-3 Mutant- T152D


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- T152D within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na302

b:19.9
occ:1.00
O F:LYS260 2.6 12.7 1.0
O F:HOH421 2.7 18.2 1.0
N B:ASP169 3.0 15.0 1.0
NE1 F:TRP206 3.1 12.4 1.0
CB F:LYS259 3.6 11.1 1.0
CA B:LEU168 3.7 11.4 1.0
CD2 B:LEU168 3.8 14.7 1.0
C F:LYS260 3.8 10.4 1.0
CD1 F:TRP206 3.8 10.7 1.0
N F:LYS260 3.8 14.2 1.0
O B:ASP169 3.8 15.5 1.0
C B:LEU168 3.8 13.6 1.0
CA B:ASP169 3.9 14.5 1.0
CB B:ASP169 3.9 13.1 1.0
CE2 F:TRP206 4.2 13.3 1.0
CB B:LEU168 4.2 15.8 1.0
C B:ASP169 4.3 19.4 1.0
C F:LYS259 4.4 12.1 1.0
CG F:LYS259 4.4 12.1 1.0
CA F:LYS260 4.5 12.6 1.0
CA F:LYS259 4.5 13.4 1.0
CG B:LEU168 4.6 15.2 1.0
CZ2 F:TRP206 4.7 13.5 1.0
O B:GLU167 4.7 13.1 1.0
N F:GLN261 4.8 11.2 1.0
N B:LEU168 4.9 14.1 1.0
CD F:LYS259 4.9 14.7 1.0
CD2 F:TYR203 5.0 11.8 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 Dec 15 11:59:13 2020

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