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Manganese in PDB 3h61: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)

Enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form):
3.1.3.16;

Protein crystallography data

The structure of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form), PDB code: 3h61 was solved by I.Bertini, V.Calderone, M.Fragai, C.Luchinat, E.Talluri, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.50 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.499, 41.781, 105.905, 90.00, 96.96, 90.00
R / Rfree (%) 16.1 / 19.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form) (pdb code 3h61). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form), PDB code: 3h61:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3h61

Go back to Manganese Binding Sites List in 3h61
Manganese binding site 1 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:6.4
occ:1.00
 O2 A:ENL0 2.0 9.2 1.0
OD1 A:ASN303 2.0 10.1 1.0
NE2 A:HIS352 2.1 5.0 1.0
ND1 A:HIS427 2.2 5.9 1.0
OD2 A:ASP271 2.3 6.3 1.0
C8 A:ENL0 2.9 8.2 1.0
O5 A:ENL0 3.0 9.5 1.0
CD2 A:HIS352 3.1 5.4 1.0
CE1 A:HIS427 3.1 6.2 1.0
CG A:ASN303 3.1 7.8 1.0
CE1 A:HIS352 3.1 5.2 1.0
CG A:ASP271 3.2 6.5 1.0
CG A:HIS427 3.3 6.0 1.0
MN A:MN501 3.4 5.7 0.9
OD1 A:ASP271 3.6 7.4 1.0
CA A:HIS427 3.7 5.9 1.0
ND2 A:ASN303 3.7 10.3 1.0
CB A:HIS427 3.8 6.0 1.0
O4 A:ENL0 4.0 8.0 1.0
OD2 A:ASP242 4.1 7.3 1.0
ND1 A:HIS352 4.2 4.9 1.0
CG A:HIS352 4.2 4.6 1.0
O A:HIS427 4.2 6.7 1.0
NE2 A:HIS427 4.3 5.3 1.0
C4 A:ENL0 4.3 8.1 1.0
CB A:ASN303 4.3 6.5 1.0
N A:ASN303 4.4 6.5 1.0
CD2 A:HIS427 4.4 6.4 1.0
C A:HIS427 4.4 6.4 1.0
CB A:ASP271 4.5 6.2 1.0
CD2 A:HIS304 4.6 9.3 1.0
O A:LEU385 4.6 7.0 1.0
N A:HIS427 4.7 5.8 1.0
C7 A:ENL0 4.7 8.5 1.0
C6 A:ENL0 4.8 8.8 1.0
O A:HOH614 4.9 23.8 1.0
CA A:ASN303 4.9 7.3 1.0
O1 A:ENL0 4.9 8.8 1.0
CG A:ASP242 4.9 6.5 1.0

Manganese binding site 2 out of 4 in 3h61

Go back to Manganese Binding Sites List in 3h61
Manganese binding site 2 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:5.7
occ:0.90
 OD2 A:ASP242 2.1 7.3 1.0
OD2 A:ASP271 2.1 6.3 1.0
NE2 A:HIS244 2.2 7.7 1.0
O4 A:ENL0 2.2 8.0 1.0
O2 A:ENL0 2.2 9.2 1.0
O1 A:ENL0 2.3 8.8 1.0
C8 A:ENL0 2.9 8.2 1.0
CE1 A:HIS244 3.1 6.8 1.0
CG A:ASP271 3.1 6.5 1.0
C6 A:ENL0 3.2 8.8 1.0
C7 A:ENL0 3.2 8.5 1.0
CD2 A:HIS244 3.2 7.2 1.0
C2 A:ENL0 3.2 9.7 1.0
CG A:ASP242 3.3 6.5 1.0
C4 A:ENL0 3.4 8.1 1.0
MN A:MN500 3.4 6.4 1.0
C3 A:ENL0 3.4 7.7 1.0
CB A:ASP271 3.5 6.2 1.0
CB A:ASP242 3.9 5.7 1.0
O5 A:ENL0 3.9 9.5 1.0
CD2 A:HIS304 4.2 9.3 1.0
OD1 A:ASP242 4.2 6.8 1.0
ND1 A:HIS244 4.2 6.9 1.0
OD1 A:ASP271 4.3 7.4 1.0
CG A:HIS244 4.3 7.7 1.0
O3 A:ENL0 4.3 12.2 1.0
NE2 A:HIS352 4.5 5.0 1.0
CE1 A:HIS352 4.5 5.2 1.0
C5 A:ENL0 4.5 9.4 1.0
C1 A:ENL0 4.5 9.6 1.0
CE1 A:PHE446 4.7 6.7 1.0
NE2 A:HIS304 4.7 9.6 1.0
CA A:HIS427 4.7 5.9 1.0
OD1 A:ASN303 4.8 10.1 1.0
CA A:ASP271 4.9 5.2 1.0
O A:HIS427 5.0 6.7 1.0

Manganese binding site 3 out of 4 in 3h61

Go back to Manganese Binding Sites List in 3h61
Manganese binding site 3 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn500

b:8.3
occ:1.00
 O2 D:ENL0 2.0 9.5 1.0
OD1 D:ASN303 2.1 9.6 1.0
NE2 D:HIS352 2.1 6.8 1.0
ND1 D:HIS427 2.2 7.6 1.0
OD2 D:ASP271 2.3 9.3 1.0
C8 D:ENL0 2.9 10.2 1.0
O5 D:ENL0 3.0 12.0 1.0
CE1 D:HIS427 3.1 7.2 1.0
CD2 D:HIS352 3.1 6.6 1.0
CG D:ASN303 3.1 8.9 1.0
CE1 D:HIS352 3.1 9.0 1.0
CG D:ASP271 3.2 8.7 1.0
CG D:HIS427 3.3 6.7 1.0
MN D:MN501 3.4 7.3 0.9
OD1 D:ASP271 3.6 9.2 1.0
ND2 D:ASN303 3.7 10.8 1.0
CA D:HIS427 3.7 7.0 1.0
CB D:HIS427 3.7 7.5 1.0
O4 D:ENL0 3.9 9.6 1.0
OD2 D:ASP242 4.0 8.6 1.0
ND1 D:HIS352 4.3 8.1 1.0
NE2 D:HIS427 4.3 7.0 1.0
CG D:HIS352 4.3 6.5 1.0
O D:HIS427 4.3 7.9 1.0
C4 D:ENL0 4.3 10.1 1.0
CB D:ASN303 4.4 9.3 1.0
CD2 D:HIS427 4.4 7.6 1.0
N D:ASN303 4.4 7.9 1.0
C D:HIS427 4.5 7.3 1.0
CB D:ASP271 4.5 8.6 1.0
CD2 D:HIS304 4.6 9.7 1.0
O D:LEU385 4.7 8.3 1.0
N D:HIS427 4.7 6.4 1.0
C7 D:ENL0 4.7 10.6 1.0
O D:HOH530 4.7 23.7 1.0
C6 D:ENL0 4.8 9.3 1.0
CA D:ASN303 4.9 9.1 1.0
CG D:ASP242 4.9 7.1 1.0
O1 D:ENL0 4.9 8.8 1.0

Manganese binding site 4 out of 4 in 3h61

Go back to Manganese Binding Sites List in 3h61
Manganese binding site 4 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Originally Soaked with Norcantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:7.3
occ:0.90
 OD2 D:ASP242 2.1 8.6 1.0
O4 D:ENL0 2.2 9.6 1.0
NE2 D:HIS244 2.2 10.4 1.0
OD2 D:ASP271 2.2 9.3 1.0
O2 D:ENL0 2.2 9.5 1.0
O1 D:ENL0 2.3 8.8 1.0
C8 D:ENL0 2.9 10.2 1.0
C6 D:ENL0 3.1 9.3 1.0
CE1 D:HIS244 3.1 10.1 1.0
C7 D:ENL0 3.1 10.6 1.0
CG D:ASP271 3.2 8.7 1.0
CD2 D:HIS244 3.2 9.4 1.0
C2 D:ENL0 3.2 10.2 1.0
CG D:ASP242 3.3 7.1 1.0
C4 D:ENL0 3.3 10.1 1.0
MN D:MN500 3.4 8.3 1.0
C3 D:ENL0 3.4 10.0 1.0
CB D:ASP271 3.5 8.6 1.0
O5 D:ENL0 3.9 12.0 1.0
CB D:ASP242 4.0 8.4 1.0
CD2 D:HIS304 4.2 9.7 1.0
OD1 D:ASP242 4.2 7.9 1.0
ND1 D:HIS244 4.2 9.7 1.0
O3 D:ENL0 4.3 12.1 1.0
OD1 D:ASP271 4.3 9.2 1.0
CG D:HIS244 4.3 9.2 1.0
C5 D:ENL0 4.4 10.5 1.0
NE2 D:HIS352 4.5 6.8 1.0
CE1 D:HIS352 4.5 9.0 1.0
C1 D:ENL0 4.5 10.7 1.0
CE1 D:PHE446 4.7 9.7 1.0
NE2 D:HIS304 4.7 10.3 1.0
CA D:HIS427 4.7 7.0 1.0
OD1 D:ASN303 4.8 9.6 1.0
CA D:ASP271 5.0 8.1 1.0
O D:HIS427 5.0 7.9 1.0

Reference:

I.Bertini, V.Calderone, M.Fragai, C.Luchinat, E.Talluri. Structural Basis of Serine/Threonine Phosphatase Inhibition By the Archetypal Small Molecules Cantharidin and Norcantharidin J.Med.Chem. V. 52 4838 2009.
ISSN: ISSN 0022-2623
PubMed: 19601647
DOI: 10.1021/JM900610K
Page generated: Sat Oct 5 16:26:31 2024

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