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Manganese in PDB 4v0u: The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex

Enzymatic activity of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex

All present enzymatic activity of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex:
3.1.3.16;

Protein crystallography data

The structure of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex, PDB code: 4v0u was solved by R.Chen, Y.Yan, A.C.Casado, D.Ron, R.J.Read, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 82.79 / 7.88
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.910, 149.930, 318.720, 90.00, 91.03, 90.00
R / Rfree (%) 37.024 / 39.976

Manganese Binding Sites:

The binding sites of Manganese atom in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex (pdb code 4v0u). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 10 binding sites of Manganese where determined in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex, PDB code: 4v0u:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 4v0u

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Manganese binding site 1 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1301

b:0.7
occ:1.00
 OD2 D:ASP64 2.0 0.7 1.0
OD2 D:ASP92 2.1 0.2 1.0
NE2 D:HIS66 2.2 0.2 1.0
MN D:MN1302 3.0 0.7 1.0
CE1 D:HIS66 3.0 0.9 1.0
CG D:ASP92 3.2 0.4 1.0
CG D:ASP64 3.2 0.8 1.0
CD2 D:HIS66 3.2 0.9 1.0
CB D:ASP92 3.6 0.7 1.0
OD1 D:ASP64 3.9 0.8 1.0
CD2 D:HIS125 4.0 0.9 1.0
ND1 D:HIS66 4.2 0.7 1.0
CB D:ASP64 4.2 0.3 1.0
OD1 D:ASP92 4.2 0.1 1.0
NE2 D:HIS125 4.3 0.9 1.0
CG D:HIS66 4.3 0.1 1.0
NE2 D:HIS173 4.3 0.8 1.0
CE1 D:HIS173 4.5 0.2 1.0
CE2 D:PHE267 4.5 0.3 1.0
ND2 D:ASN124 4.6 0.1 1.0
OH D:TYR272 4.6 0.7 1.0
CA D:HIS248 4.7 0.9 1.0
ND1 D:HIS248 4.8 0.2 1.0
CG D:HIS125 5.0 0.3 1.0

Manganese binding site 2 out of 10 in 4v0u

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Manganese binding site 2 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn1302

b:0.7
occ:1.00
 ND2 D:ASN124 2.1 0.1 1.0
OD2 D:ASP92 2.2 0.2 1.0
NE2 D:HIS173 2.3 0.8 1.0
ND1 D:HIS248 2.3 0.2 1.0
MN D:MN1301 3.0 0.7 1.0
CE1 D:HIS248 3.1 0.5 1.0
CG D:ASP92 3.2 0.4 1.0
CG D:ASN124 3.2 0.5 1.0
CE1 D:HIS173 3.2 0.2 1.0
CD2 D:HIS173 3.2 0.2 1.0
CG D:HIS248 3.4 0.7 1.0
OD1 D:ASP92 3.6 0.1 1.0
OD1 D:ASN124 3.6 0.2 1.0
CA D:HIS248 3.7 0.9 1.0
CB D:HIS248 3.8 0.1 1.0
OD2 D:ASP64 4.0 0.7 1.0
CD2 D:HIS125 4.2 0.9 1.0
NE2 D:HIS248 4.3 0.4 1.0
ND1 D:HIS173 4.4 1.0 1.0
CG D:HIS173 4.4 0.8 1.0
O D:HIS248 4.4 0.8 1.0
CB D:ASP92 4.4 0.7 1.0
CB D:ASN124 4.5 0.2 1.0
CD2 D:HIS248 4.5 0.0 1.0
C D:HIS248 4.5 0.4 1.0
N D:ASN124 4.6 0.3 1.0
N D:HIS248 4.7 0.8 1.0
OD1 D:ASP64 4.7 0.8 1.0
CG D:ASP64 4.8 0.8 1.0
NE2 D:HIS125 4.8 0.9 1.0
O D:LEU205 4.9 0.6 1.0
NE2 D:HIS66 4.9 0.2 1.0

Manganese binding site 3 out of 10 in 4v0u

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Manganese binding site 3 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1301

b:0.1
occ:1.00
 OD2 F:ASP64 2.0 0.9 1.0
OD2 F:ASP92 2.1 0.3 1.0
NE2 F:HIS66 2.2 0.9 1.0
MN F:MN1302 3.0 0.6 1.0
CE1 F:HIS66 3.0 0.1 1.0
CG F:ASP92 3.2 0.6 1.0
CG F:ASP64 3.2 0.4 1.0
CD2 F:HIS66 3.2 0.9 1.0
CB F:ASP92 3.6 0.2 1.0
OD1 F:ASP64 3.9 0.9 1.0
CD2 F:HIS125 4.0 0.2 1.0
ND1 F:HIS66 4.2 0.1 1.0
CB F:ASP64 4.2 0.7 1.0
OD1 F:ASP92 4.2 0.0 1.0
NE2 F:HIS125 4.3 0.6 1.0
CG F:HIS66 4.3 0.0 1.0
NE2 F:HIS173 4.3 0.3 1.0
CE1 F:HIS173 4.5 0.0 1.0
CE2 F:PHE267 4.5 0.4 1.0
ND2 F:ASN124 4.6 0.1 1.0
OH F:TYR272 4.6 0.5 1.0
CA F:HIS248 4.7 0.7 1.0
ND1 F:HIS248 4.8 0.6 1.0
CG F:HIS125 5.0 0.3 1.0

Manganese binding site 4 out of 10 in 4v0u

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Manganese binding site 4 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn1302

b:0.6
occ:1.00
 ND2 F:ASN124 2.1 0.1 1.0
OD2 F:ASP92 2.2 0.3 1.0
NE2 F:HIS173 2.3 0.3 1.0
ND1 F:HIS248 2.3 0.6 1.0
MN F:MN1301 3.0 0.1 1.0
CE1 F:HIS248 3.1 0.2 1.0
CG F:ASP92 3.2 0.6 1.0
CG F:ASN124 3.2 0.3 1.0
CE1 F:HIS173 3.2 0.0 1.0
CD2 F:HIS173 3.2 0.8 1.0
CG F:HIS248 3.4 0.0 1.0
OD1 F:ASP92 3.6 0.0 1.0
OD1 F:ASN124 3.6 0.1 1.0
CA F:HIS248 3.7 0.7 1.0
CB F:HIS248 3.8 0.4 1.0
OD2 F:ASP64 4.0 0.9 1.0
CD2 F:HIS125 4.2 0.2 1.0
NE2 F:HIS248 4.3 0.6 1.0
ND1 F:HIS173 4.4 0.0 1.0
CG F:HIS173 4.4 0.9 1.0
O F:HIS248 4.4 0.5 1.0
CB F:ASP92 4.4 0.2 1.0
CB F:ASN124 4.5 0.4 1.0
CD2 F:HIS248 4.5 0.2 1.0
C F:HIS248 4.5 0.3 1.0
N F:ASN124 4.6 0.2 1.0
N F:HIS248 4.7 0.3 1.0
OD1 F:ASP64 4.7 0.9 1.0
CG F:ASP64 4.7 0.4 1.0
NE2 F:HIS125 4.8 0.6 1.0
O F:LEU205 4.9 0.1 1.0
NE2 F:HIS66 4.9 0.9 1.0

Manganese binding site 5 out of 10 in 4v0u

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Manganese binding site 5 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1301

b:0.3
occ:1.00
 OD2 H:ASP64 2.0 0.0 1.0
OD2 H:ASP92 2.1 0.0 1.0
NE2 H:HIS66 2.2 0.7 1.0
MN H:MN1302 3.0 0.8 1.0
CE1 H:HIS66 3.0 0.8 1.0
CG H:ASP92 3.2 0.7 1.0
CG H:ASP64 3.2 0.8 1.0
CD2 H:HIS66 3.2 0.8 1.0
CB H:ASP92 3.6 0.5 1.0
OD1 H:ASP64 3.9 0.5 1.0
CD2 H:HIS125 4.0 0.7 1.0
ND1 H:HIS66 4.2 0.6 1.0
CB H:ASP64 4.2 0.9 1.0
OD1 H:ASP92 4.2 0.3 1.0
NE2 H:HIS125 4.3 0.6 1.0
CG H:HIS66 4.3 0.3 1.0
NE2 H:HIS173 4.3 0.3 1.0
CE1 H:HIS173 4.5 0.7 1.0
CE2 H:PHE267 4.5 0.5 1.0
ND2 H:ASN124 4.6 0.0 1.0
OH H:TYR272 4.6 0.3 1.0
CA H:HIS248 4.7 0.8 1.0
ND1 H:HIS248 4.8 0.1 1.0
CG H:HIS125 5.0 0.0 1.0

Manganese binding site 6 out of 10 in 4v0u

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Manganese binding site 6 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Mn1302

b:0.8
occ:1.00
 ND2 H:ASN124 2.1 0.0 1.0
OD2 H:ASP92 2.2 0.0 1.0
NE2 H:HIS173 2.3 0.3 1.0
ND1 H:HIS248 2.3 0.1 1.0
MN H:MN1301 3.0 0.3 1.0
CE1 H:HIS248 3.1 0.0 1.0
CG H:ASP92 3.2 0.7 1.0
CG H:ASN124 3.2 0.9 1.0
CE1 H:HIS173 3.2 0.7 1.0
CD2 H:HIS173 3.2 0.3 1.0
CG H:HIS248 3.4 0.4 1.0
OD1 H:ASP92 3.6 0.3 1.0
OD1 H:ASN124 3.6 0.5 1.0
CA H:HIS248 3.7 0.8 1.0
CB H:HIS248 3.8 0.9 1.0
OD2 H:ASP64 4.0 0.0 1.0
CD2 H:HIS125 4.2 0.7 1.0
NE2 H:HIS248 4.3 0.7 1.0
ND1 H:HIS173 4.4 0.2 1.0
CG H:HIS173 4.4 0.7 1.0
O H:HIS248 4.4 0.0 1.0
CB H:ASP92 4.4 0.5 1.0
CB H:ASN124 4.5 0.7 1.0
CD2 H:HIS248 4.5 0.7 1.0
C H:HIS248 4.5 0.2 1.0
N H:ASN124 4.6 0.1 1.0
N H:HIS248 4.7 0.3 1.0
OD1 H:ASP64 4.7 0.5 1.0
CG H:ASP64 4.8 0.8 1.0
NE2 H:HIS125 4.8 0.6 1.0
O H:LEU205 4.9 0.3 1.0
NE2 H:HIS66 5.0 0.7 1.0

Manganese binding site 7 out of 10 in 4v0u

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Manganese binding site 7 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 7 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1301

b:0.7
occ:1.00
 OD2 J:ASP64 2.0 0.6 1.0
OD2 J:ASP92 2.1 0.8 1.0
NE2 J:HIS66 2.2 0.7 1.0
MN J:MN1302 3.0 1.0 1.0
CE1 J:HIS66 3.0 0.7 1.0
CG J:ASP92 3.2 0.3 1.0
CG J:ASP64 3.2 0.2 1.0
CD2 J:HIS66 3.2 0.8 1.0
CB J:ASP92 3.6 1.0 1.0
OD1 J:ASP64 3.9 0.2 1.0
CD2 J:HIS125 4.0 0.7 1.0
ND1 J:HIS66 4.2 0.7 1.0
CB J:ASP64 4.2 0.3 1.0
OD1 J:ASP92 4.2 0.8 1.0
NE2 J:HIS125 4.3 0.6 1.0
CG J:HIS66 4.3 0.3 1.0
NE2 J:HIS173 4.3 0.5 1.0
CE1 J:HIS173 4.5 0.2 1.0
CE2 J:PHE267 4.5 0.1 1.0
ND2 J:ASN124 4.6 0.7 1.0
OH J:TYR272 4.6 0.2 1.0
CA J:HIS248 4.7 0.2 1.0
ND1 J:HIS248 4.8 0.2 1.0
CG J:HIS125 5.0 0.4 1.0

Manganese binding site 8 out of 10 in 4v0u

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Manganese binding site 8 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 8 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Mn1302

b:1.0
occ:1.00
 ND2 J:ASN124 2.1 0.7 1.0
OD2 J:ASP92 2.2 0.8 1.0
NE2 J:HIS173 2.3 0.5 1.0
ND1 J:HIS248 2.3 0.2 1.0
MN J:MN1301 3.0 0.7 1.0
CE1 J:HIS248 3.1 0.4 1.0
CG J:ASP92 3.2 0.3 1.0
CG J:ASN124 3.2 0.4 1.0
CE1 J:HIS173 3.2 0.2 1.0
CD2 J:HIS173 3.2 0.2 1.0
CG J:HIS248 3.4 1.0 1.0
OD1 J:ASP92 3.6 0.8 1.0
OD1 J:ASN124 3.6 0.7 1.0
CA J:HIS248 3.7 0.2 1.0
CB J:HIS248 3.8 0.5 1.0
OD2 J:ASP64 4.0 0.6 1.0
CD2 J:HIS125 4.2 0.7 1.0
NE2 J:HIS248 4.3 0.6 1.0
ND1 J:HIS173 4.4 0.8 1.0
CG J:HIS173 4.4 0.2 1.0
O J:HIS248 4.4 0.9 1.0
CB J:ASP92 4.4 1.0 1.0
CB J:ASN124 4.5 0.4 1.0
CD2 J:HIS248 4.5 0.6 1.0
C J:HIS248 4.5 0.9 1.0
N J:ASN124 4.6 0.8 1.0
N J:HIS248 4.7 0.1 1.0
OD1 J:ASP64 4.7 0.2 1.0
CG J:ASP64 4.8 0.2 1.0
NE2 J:HIS125 4.8 0.6 1.0
O J:LEU205 4.9 0.5 1.0
NE2 J:HIS66 4.9 0.7 1.0

Manganese binding site 9 out of 10 in 4v0u

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Manganese binding site 9 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mn1301

b:0.1
occ:1.00
 OD2 N:ASP64 2.0 0.5 1.0
OD2 N:ASP92 2.1 0.9 1.0
NE2 N:HIS66 2.2 0.6 1.0
MN N:MN1302 3.0 0.9 1.0
CE1 N:HIS66 3.0 0.9 1.0
CG N:ASP92 3.2 0.8 1.0
CG N:ASP64 3.2 0.1 1.0
CD2 N:HIS66 3.2 0.9 1.0
CB N:ASP92 3.6 0.1 1.0
OD1 N:ASP64 3.9 0.8 1.0
CD2 N:HIS125 4.0 0.7 1.0
ND1 N:HIS66 4.2 0.7 1.0
CB N:ASP64 4.2 0.0 1.0
OD1 N:ASP92 4.2 0.7 1.0
NE2 N:HIS125 4.3 0.1 1.0
CG N:HIS66 4.3 0.8 1.0
NE2 N:HIS173 4.3 0.1 1.0
CE1 N:HIS173 4.5 0.7 1.0
CE2 N:PHE267 4.5 0.7 1.0
ND2 N:ASN124 4.6 0.3 1.0
OH N:TYR272 4.6 0.9 1.0
CA N:HIS248 4.7 0.3 1.0
ND1 N:HIS248 4.8 0.8 1.0
CG N:HIS125 5.0 0.8 1.0

Manganese binding site 10 out of 10 in 4v0u

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Manganese binding site 10 out of 10 in the The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of The Crystal Structure of Ternary PP1G-PPP1R15B and G-Actin Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Mn1302

b:0.9
occ:1.00
 ND2 N:ASN124 2.1 0.3 1.0
OD2 N:ASP92 2.2 0.9 1.0
NE2 N:HIS173 2.3 0.1 1.0
ND1 N:HIS248 2.3 0.8 1.0
MN N:MN1301 3.0 0.1 1.0
CE1 N:HIS248 3.1 0.2 1.0
CG N:ASP92 3.2 0.8 1.0
CG N:ASN124 3.2 0.9 1.0
CE1 N:HIS173 3.2 0.7 1.0
CD2 N:HIS173 3.3 0.8 1.0
CG N:HIS248 3.4 0.7 1.0
OD1 N:ASP92 3.6 0.7 1.0
OD1 N:ASN124 3.6 0.5 1.0
CA N:HIS248 3.7 0.3 1.0
CB N:HIS248 3.8 0.6 1.0
OD2 N:ASP64 4.0 0.5 1.0
CD2 N:HIS125 4.2 0.7 1.0
NE2 N:HIS248 4.3 0.9 1.0
ND1 N:HIS173 4.4 0.7 1.0
CG N:HIS173 4.4 0.7 1.0
O N:HIS248 4.4 0.6 1.0
CB N:ASP92 4.4 0.1 1.0
CD2 N:HIS248 4.5 0.4 1.0
CB N:ASN124 4.5 0.6 1.0
C N:HIS248 4.5 0.6 1.0
N N:ASN124 4.6 0.2 1.0
N N:HIS248 4.7 0.4 1.0
OD1 N:ASP64 4.7 0.8 1.0
CG N:ASP64 4.8 0.1 1.0
NE2 N:HIS125 4.8 0.1 1.0
O N:LEU205 4.9 0.4 1.0
NE2 N:HIS66 4.9 0.6 1.0

Reference:

R.Chen, C.Rato, Y.Yan, A.Crespillo-Casado, H.J.Clarke, H.P.Harding, S.J.Marciniak, R.J.Read, D.Ron. G-Actin Provides Substrate-Specificity to Eukaryotic Initiation Factor 2ALPHA Holophosphatases. Elife V. 4 2015.
ISSN: ISSN 2050-084X
PubMed: 25774600
DOI: 10.7554/ELIFE.04871
Page generated: Sat Oct 5 21:28:58 2024

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