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Zinc in PDB 3h68: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form)

Enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (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 ZN2+ Atoms Originally Soaked with Cantharidin (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 ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form), PDB code: 3h68 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) 38.24 / 1.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.175, 41.721, 105.172, 90.00, 97.24, 90.00
R / Rfree (%) 18.4 / 23.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form) (pdb code 3h68). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form), PDB code: 3h68:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3h68

Go back to Zinc Binding Sites List in 3h68
Zinc binding site 1 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:11.2
occ:0.90
 O3 A:NHC1 2.0 9.7 0.4
O3 A:NHC1 2.0 10.0 0.4
NE2 A:HIS352 2.0 10.3 1.0
OD1 A:ASN303 2.1 13.2 1.0
ND1 A:HIS427 2.1 11.0 1.0
OD2 A:ASP271 2.4 9.6 1.0
C9 A:NHC1 2.7 11.1 0.4
C9 A:NHC1 2.8 9.7 0.4
O5 A:NHC1 2.8 9.4 0.4
CE1 A:HIS352 2.9 8.2 1.0
O5 A:NHC1 3.0 12.5 0.4
CE1 A:HIS427 3.0 10.2 1.0
CD2 A:HIS352 3.1 12.3 1.0
CG A:ASN303 3.1 9.5 1.0
CG A:HIS427 3.2 8.8 1.0
CG A:ASP271 3.2 9.4 1.0
ZN A:ZN501 3.3 13.6 0.9
ND2 A:ASN303 3.6 9.4 1.0
CA A:HIS427 3.6 10.9 1.0
OD1 A:ASP271 3.6 9.4 1.0
O2 A:NHC1 3.6 9.9 0.4
CB A:HIS427 3.6 9.3 1.0
O4 A:NHC1 3.9 12.7 0.4
OD2 A:ASP242 4.0 12.4 1.0
ND1 A:HIS352 4.1 7.4 1.0
C4 A:NHC1 4.1 11.0 0.4
C8 A:NHC1 4.1 11.6 0.4
CG A:HIS352 4.2 9.9 1.0
C4 A:NHC1 4.2 13.0 0.4
NE2 A:HIS427 4.2 10.5 1.0
O2 A:NHC1 4.2 9.6 0.4
O A:HIS427 4.2 11.7 1.0
CD2 A:HIS427 4.3 9.9 1.0
C A:HIS427 4.4 9.8 1.0
CB A:ASN303 4.4 9.5 1.0
N A:ASN303 4.4 10.3 1.0
C6 A:NHC1 4.5 10.9 0.4
CB A:ASP271 4.5 10.0 1.0
C8 A:NHC1 4.6 7.0 0.4
O A:LEU385 4.6 9.2 1.0
N A:HIS427 4.6 9.8 1.0
C6 A:NHC1 4.6 13.9 0.4
CD2 A:HIS304 4.7 12.5 1.0
O1 A:NHC1 4.7 10.6 0.4
O1 A:NHC1 4.8 13.2 0.4
CG A:ASP242 4.8 10.5 1.0
C10 A:NHC1 4.9 10.4 0.4
C3 A:NHC1 4.9 12.2 0.4
CA A:ASN303 4.9 10.3 1.0
OD1 A:ASP242 5.0 10.4 1.0
C3 A:NHC1 5.0 8.7 0.4

Zinc binding site 2 out of 4 in 3h68

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Zinc binding site 2 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:13.6
occ:0.90
 O3 A:NHC1 1.9 9.7 0.4
OD2 A:ASP242 2.0 12.4 1.0
OD2 A:ASP271 2.1 9.6 1.0
NE2 A:HIS244 2.1 13.2 1.0
O1 A:NHC1 2.1 10.6 0.4
O3 A:NHC1 2.2 10.0 0.4
O2 A:NHC1 2.2 9.9 0.4
O1 A:NHC1 2.3 13.2 0.4
O2 A:NHC1 2.4 9.6 0.4
C9 A:NHC1 2.8 9.7 0.4
C6 A:NHC1 2.9 10.9 0.4
C2 A:NHC1 2.9 10.0 0.4
C9 A:NHC1 2.9 11.1 0.4
C8 A:NHC1 3.0 11.6 0.4
CE1 A:HIS244 3.0 15.0 1.0
C8 A:NHC1 3.0 7.0 0.4
CG A:ASP271 3.1 9.4 1.0
C2 A:NHC1 3.1 13.8 0.4
C4 A:NHC1 3.1 11.0 0.4
C6 A:NHC1 3.1 13.9 0.4
CD2 A:HIS244 3.1 12.8 1.0
CG A:ASP242 3.2 10.5 1.0
C3 A:NHC1 3.2 8.7 0.4
ZN A:ZN500 3.3 11.2 0.9
C3 A:NHC1 3.4 12.2 0.4
C4 A:NHC1 3.4 13.0 0.4
CB A:ASP271 3.5 10.0 1.0
O4 A:NHC1 3.8 12.7 0.4
CB A:ASP242 3.9 10.3 1.0
O5 A:NHC1 4.0 12.5 0.4
O5 A:NHC1 4.0 9.4 0.4
OD1 A:ASP242 4.1 10.4 1.0
ND1 A:HIS244 4.2 13.3 1.0
O4 A:NHC1 4.2 9.9 0.4
OD1 A:ASP271 4.2 9.4 1.0
C5 A:NHC1 4.2 9.8 0.4
C1 A:NHC1 4.2 11.2 0.4
CG A:HIS244 4.3 12.4 1.0
CD2 A:HIS304 4.3 12.5 1.0
CE1 A:HIS352 4.3 8.2 1.0
NE2 A:HIS352 4.4 10.3 1.0
C1 A:NHC1 4.4 13.6 0.4
C5 A:NHC1 4.4 12.7 0.4
C10 A:NHC1 4.6 10.4 0.4
OD1 A:ASN303 4.7 13.2 1.0
CA A:HIS427 4.7 10.9 1.0
CE1 A:PHE446 4.7 13.3 1.0
NE2 A:HIS304 4.7 13.9 1.0
C7 A:NHC1 4.7 9.7 0.4
NH1 A:ARG275 4.8 38.3 1.0
C7 A:NHC1 4.9 12.6 0.4
C10 A:NHC1 4.9 12.7 0.4
CA A:ASP271 4.9 8.9 1.0

Zinc binding site 3 out of 4 in 3h68

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Zinc binding site 3 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:15.8
occ:0.90
 O3 D:NHC1 2.0 11.1 0.4
NE2 D:HIS352 2.0 13.7 1.0
OD1 D:ASN303 2.1 18.2 1.0
O3 D:NHC1 2.2 13.8 0.4
ND1 D:HIS427 2.2 16.2 1.0
OD2 D:ASP271 2.3 13.9 1.0
C9 D:NHC1 2.9 15.7 0.4
O5 D:NHC1 2.9 13.5 0.4
C9 D:NHC1 3.0 11.9 0.4
CE1 D:HIS352 3.0 15.0 1.0
CE1 D:HIS427 3.0 17.6 1.0
CD2 D:HIS352 3.1 14.9 1.0
CG D:ASN303 3.1 15.2 1.0
CG D:ASP271 3.2 14.7 1.0
O5 D:NHC1 3.3 14.5 0.4
CG D:HIS427 3.3 16.1 1.0
ZN D:ZN501 3.3 17.7 0.9
ND2 D:ASN303 3.5 17.2 1.0
OD1 D:ASP271 3.6 15.8 1.0
CA D:HIS427 3.6 15.3 1.0
CB D:HIS427 3.7 14.9 1.0
OD2 D:ASP242 3.8 15.2 1.0
O2 D:NHC1 3.8 14.4 0.4
O2 D:NHC1 4.0 18.4 0.4
ND1 D:HIS352 4.1 13.8 1.0
CG D:HIS352 4.2 14.1 1.0
NE2 D:HIS427 4.2 18.1 1.0
O D:HIS427 4.2 14.9 1.0
C8 D:NHC1 4.2 18.6 0.4
C4 D:NHC1 4.3 17.1 0.4
O4 D:NHC1 4.3 18.6 0.4
C4 D:NHC1 4.4 13.5 0.4
CD2 D:HIS427 4.4 16.9 1.0
C D:HIS427 4.4 14.8 1.0
CB D:ASN303 4.4 15.9 1.0
CB D:ASP271 4.5 15.6 1.0
N D:ASN303 4.5 15.7 1.0
O D:LEU385 4.6 13.2 1.0
N D:HIS427 4.6 14.3 1.0
CD2 D:HIS304 4.6 18.3 1.0
C6 D:NHC1 4.7 14.7 0.4
C8 D:NHC1 4.7 15.0 0.4
CG D:ASP242 4.8 12.8 1.0
C6 D:NHC1 4.8 18.5 0.4
O1 D:NHC1 4.9 13.8 0.4
O1 D:NHC1 4.9 18.5 0.4
CA D:ASN303 5.0 15.8 1.0

Zinc binding site 4 out of 4 in 3h68

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Zinc binding site 4 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Originally Soaked with Cantharidin (Which Is Present in the Structure in the Hydrolyzed Form) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:17.7
occ:0.90
 OD2 D:ASP271 2.1 13.9 1.0
NE2 D:HIS244 2.1 17.4 1.0
OD2 D:ASP242 2.1 15.2 1.0
O2 D:NHC1 2.2 14.4 0.4
O1 D:NHC1 2.2 13.8 0.4
O3 D:NHC1 2.3 11.1 0.4
O3 D:NHC1 2.3 13.8 0.4
O2 D:NHC1 2.4 18.4 0.4
O1 D:NHC1 2.4 18.5 0.4
C9 D:NHC1 2.7 11.9 0.4
C9 D:NHC1 3.0 15.7 0.4
CE1 D:HIS244 3.0 19.4 1.0
C6 D:NHC1 3.0 14.7 0.4
CG D:ASP271 3.1 14.7 1.0
C8 D:NHC1 3.1 18.6 0.4
CD2 D:HIS244 3.1 16.0 1.0
C8 D:NHC1 3.1 15.0 0.4
C2 D:NHC1 3.1 15.3 0.4
C6 D:NHC1 3.2 18.5 0.4
C2 D:NHC1 3.2 18.5 0.4
C4 D:NHC1 3.3 13.5 0.4
CG D:ASP242 3.3 12.8 1.0
ZN D:ZN500 3.3 15.8 0.9
O5 D:NHC1 3.4 14.5 0.4
C3 D:NHC1 3.4 14.8 0.4
CB D:ASP271 3.4 15.6 1.0
C4 D:NHC1 3.5 17.1 0.4
C3 D:NHC1 3.5 17.9 0.4
O5 D:NHC1 3.8 13.5 0.4
CB D:ASP242 3.9 15.8 1.0
O4 D:NHC1 4.1 18.6 0.4
ND1 D:HIS244 4.1 17.4 1.0
OD1 D:ASP271 4.2 15.8 1.0
CG D:HIS244 4.2 17.2 1.0
OD1 D:ASP242 4.3 13.6 1.0
O4 D:NHC1 4.3 15.6 0.4
C5 D:NHC1 4.3 14.9 0.4
CD2 D:HIS304 4.3 18.3 1.0
CE1 D:HIS352 4.4 15.0 1.0
C1 D:NHC1 4.4 15.4 0.4
NE2 D:HIS352 4.4 13.7 1.0
C5 D:NHC1 4.5 18.5 0.4
C1 D:NHC1 4.5 18.7 0.4
NH1 D:ARG275 4.6 36.0 1.0
C10 D:NHC1 4.7 13.2 0.4
CE1 D:PHE446 4.7 17.5 1.0
OD1 D:ASN303 4.8 18.2 1.0
CA D:HIS427 4.8 15.3 1.0
NE2 D:HIS304 4.8 18.2 1.0
CA D:ASP271 4.9 14.7 1.0
C7 D:NHC1 5.0 15.4 0.4
C10 D:NHC1 5.0 17.1 0.4

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: Thu Oct 24 14:15:51 2024

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