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Zinc in PDB 3h67: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid

Enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid:
3.1.3.16;

Protein crystallography data

The structure of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid, PDB code: 3h67 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) 39.44 / 1.65
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 158.875, 41.775, 104.989, 90.00, 96.96, 90.00
R / Rfree (%) 18.1 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid (pdb code 3h67). 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 Complexed with Cantharidic Acid, PDB code: 3h67:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3h67

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Zinc binding site 1 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two ZN2+ Atoms Complexed with Cantharidic Acid


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:12.0
occ:0.90
 NE2 A:HIS352 2.0 11.0 1.0
O3 A:NHC1 2.0 7.5 0.4
OD1 A:ASN303 2.1 14.6 1.0
ND1 A:HIS427 2.2 13.0 1.0
O3 A:NHC1 2.2 10.6 0.4
OD2 A:ASP271 2.5 7.9 1.0
CE1 A:HIS352 2.9 8.4 1.0
C9 A:NHC1 3.0 13.2 0.4
CD2 A:HIS352 3.0 15.8 1.0
O5 A:NHC1 3.0 12.0 0.4
C9 A:NHC1 3.1 8.2 0.4
CG A:ASN303 3.1 12.9 1.0
CE1 A:HIS427 3.1 11.2 1.0
CG A:HIS427 3.2 10.1 1.0
O5 A:NHC1 3.4 8.0 0.4
ZN A:ZN501 3.4 15.7 0.9
CG A:ASP271 3.4 8.8 1.0
ND2 A:ASN303 3.5 12.7 1.0
CA A:HIS427 3.6 10.0 1.0
CB A:HIS427 3.6 10.0 1.0
OD1 A:ASP271 3.7 9.4 1.0
O2 A:NHC1 3.8 5.2 0.4
OD2 A:ASP242 4.0 13.9 1.0
O4 A:NHC1 4.0 15.2 0.4
ND1 A:HIS352 4.0 9.0 1.0
CG A:HIS352 4.1 8.6 1.0
NE2 A:HIS427 4.3 12.6 1.0
C8 A:NHC1 4.3 13.7 0.4
O A:HIS427 4.3 11.5 1.0
CD2 A:HIS427 4.4 13.2 1.0
O2 A:NHC1 4.4 10.6 0.4
CB A:ASN303 4.4 11.9 1.0
C A:HIS427 4.4 9.6 1.0
C4 A:NHC1 4.5 8.9 0.4
C4 A:NHC1 4.5 14.7 0.4
N A:ASN303 4.5 12.4 1.0
N A:HIS427 4.6 9.7 1.0
O A:LEU385 4.6 10.5 1.0
CD2 A:HIS304 4.7 12.4 1.0
CB A:ASP271 4.7 10.0 1.0
C6 A:NHC1 4.7 8.3 0.4
C8 A:NHC1 4.9 6.5 0.4
O1 A:NHC1 4.9 5.7 0.4
CG A:ASP242 4.9 10.4 1.0
C6 A:NHC1 4.9 14.8 0.4
O1 A:NHC1 5.0 13.9 0.4
CA A:ASN303 5.0 11.9 1.0

Zinc binding site 2 out of 4 in 3h67

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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 Complexed with Cantharidic Acid


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:15.7
occ:0.90
 OD2 A:ASP242 2.1 13.9 1.0
NE2 A:HIS244 2.2 11.8 1.0
OD2 A:ASP271 2.2 7.9 1.0
O3 A:NHC1 2.3 7.5 0.4
O1 A:NHC1 2.3 5.7 0.4
O3 A:NHC1 2.3 10.6 0.4
O2 A:NHC1 2.4 5.2 0.4
O1 A:NHC1 2.5 13.9 0.4
O2 A:NHC1 2.6 10.6 0.4
C9 A:NHC1 2.8 8.2 0.4
CE1 A:HIS244 3.0 15.3 1.0
C9 A:NHC1 3.1 13.2 0.4
C6 A:NHC1 3.1 8.3 0.4
C8 A:NHC1 3.2 13.7 0.4
C2 A:NHC1 3.2 6.6 0.4
CG A:ASP271 3.2 8.8 1.0
C8 A:NHC1 3.3 6.5 0.4
CG A:ASP242 3.3 10.4 1.0
CD2 A:HIS244 3.3 13.2 1.0
C4 A:NHC1 3.3 8.9 0.4
C2 A:NHC1 3.4 14.8 0.4
ZN A:ZN500 3.4 12.0 0.9
C6 A:NHC1 3.4 14.8 0.4
C3 A:NHC1 3.5 6.2 0.4
CB A:ASP271 3.6 10.0 1.0
C4 A:NHC1 3.6 14.7 0.4
C3 A:NHC1 3.6 14.0 0.4
O5 A:NHC1 3.7 8.0 0.4
O4 A:NHC1 3.9 15.2 0.4
O5 A:NHC1 4.0 12.0 0.4
CB A:ASP242 4.0 11.7 1.0
NH2 A:ARG275 4.1 28.7 0.5
ND1 A:HIS244 4.2 13.1 1.0
OD1 A:ASP242 4.2 10.4 1.0
CE1 A:HIS352 4.2 8.4 1.0
OD1 A:ASP271 4.3 9.4 1.0
CD2 A:HIS304 4.3 12.4 1.0
CG A:HIS244 4.3 12.6 1.0
NE2 A:HIS352 4.4 11.0 1.0
O4 A:NHC1 4.4 11.9 0.4
C5 A:NHC1 4.4 7.4 0.4
C1 A:NHC1 4.4 7.7 0.4
C1 A:NHC1 4.7 14.1 0.4
C5 A:NHC1 4.7 15.2 0.4
CA A:HIS427 4.7 10.0 1.0
CE1 A:PHE446 4.8 13.5 1.0
OD1 A:ASN303 4.8 14.6 1.0
C10 A:NHC1 4.8 7.2 0.4
NE2 A:HIS304 4.8 12.1 1.0

Zinc binding site 3 out of 4 in 3h67

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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 Complexed with Cantharidic Acid


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:18.2
occ:0.90
 O3 D:NHC1 1.9 11.7 0.4
OD1 D:ASN303 2.0 21.4 1.0
NE2 D:HIS352 2.1 14.1 1.0
ND1 D:HIS427 2.2 16.7 1.0
O3 D:NHC1 2.2 16.0 0.4
OD2 D:ASP271 2.4 15.5 1.0
O5 D:NHC1 2.7 15.3 0.4
C9 D:NHC1 2.8 18.1 0.4
CE1 D:HIS352 3.0 16.3 1.0
CE1 D:HIS427 3.0 17.7 1.0
C9 D:NHC1 3.1 12.5 0.4
CG D:ASN303 3.1 19.8 1.0
CD2 D:HIS352 3.2 14.3 1.0
CG D:HIS427 3.3 18.6 1.0
CG D:ASP271 3.3 16.9 1.0
ZN D:ZN501 3.3 23.3 0.9
O5 D:NHC1 3.5 11.2 0.4
ND2 D:ASN303 3.5 20.1 1.0
OD1 D:ASP271 3.6 19.1 1.0
CA D:HIS427 3.7 18.1 1.0
CB D:HIS427 3.7 17.8 1.0
O2 D:NHC1 3.7 14.4 0.4
OD2 D:ASP242 3.9 19.1 1.0
O2 D:NHC1 3.9 11.9 0.4
ND1 D:HIS352 4.2 14.4 1.0
C8 D:NHC1 4.2 18.8 0.4
NE2 D:HIS427 4.2 19.1 1.0
O D:HIS427 4.2 18.0 1.0
CG D:HIS352 4.3 14.1 1.0
C4 D:NHC1 4.3 18.9 0.4
CD2 D:HIS427 4.4 18.6 1.0
C4 D:NHC1 4.4 13.1 0.4
C D:HIS427 4.4 17.8 1.0
CB D:ASN303 4.4 19.4 1.0
CD2 D:HIS304 4.5 20.6 1.0
CB D:ASP271 4.6 18.0 1.0
O4 D:NHC1 4.6 18.4 0.4
N D:ASN303 4.6 19.0 1.0
N D:HIS427 4.6 17.2 1.0
O D:LEU385 4.7 17.4 1.0
C6 D:NHC1 4.7 13.3 0.4
C8 D:NHC1 4.8 13.2 0.4
O1 D:NHC1 4.8 20.7 0.4
C6 D:NHC1 4.8 20.0 0.4
CG D:ASP242 4.9 19.2 1.0
C3 D:NHC1 4.9 19.5 0.4
O1 D:NHC1 5.0 12.2 0.4

Zinc binding site 4 out of 4 in 3h67

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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 Complexed with Cantharidic Acid


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:23.3
occ:0.90
 OD2 D:ASP271 2.1 15.5 1.0
NE2 D:HIS244 2.1 16.6 1.0
O2 D:NHC1 2.2 11.9 0.4
OD2 D:ASP242 2.2 19.1 1.0
O1 D:NHC1 2.3 12.2 0.4
O3 D:NHC1 2.3 16.0 0.4
O3 D:NHC1 2.3 11.7 0.4
O2 D:NHC1 2.4 14.4 0.4
O1 D:NHC1 2.4 20.7 0.4
C9 D:NHC1 2.8 12.5 0.4
CE1 D:HIS244 2.9 19.5 1.0
C6 D:NHC1 3.0 13.3 0.4
C9 D:NHC1 3.0 18.1 0.4
CG D:ASP271 3.2 16.9 1.0
C8 D:NHC1 3.2 13.2 0.4
C2 D:NHC1 3.2 19.9 0.4
C2 D:NHC1 3.3 13.2 0.4
CD2 D:HIS244 3.3 18.2 1.0
C4 D:NHC1 3.3 13.1 0.4
ZN D:ZN500 3.3 18.2 0.9
C8 D:NHC1 3.3 18.8 0.4
C6 D:NHC1 3.4 20.0 0.4
CG D:ASP242 3.4 19.2 1.0
C3 D:NHC1 3.5 13.3 0.4
O5 D:NHC1 3.5 11.2 0.4
C4 D:NHC1 3.6 18.9 0.4
CB D:ASP271 3.6 18.0 1.0
C3 D:NHC1 3.6 19.5 0.4
O5 D:NHC1 3.8 15.3 0.4
CB D:ASP242 4.0 18.6 1.0
ND1 D:HIS244 4.1 19.6 1.0
NH2 D:ARG275 4.2 42.6 0.5
OD1 D:ASP271 4.3 19.1 1.0
CD2 D:HIS304 4.3 20.6 1.0
CG D:HIS244 4.3 19.4 1.0
O4 D:NHC1 4.3 12.1 0.4
CE1 D:HIS352 4.3 16.3 1.0
OD1 D:ASP242 4.4 21.0 1.0
C5 D:NHC1 4.4 13.5 0.4
NE2 D:HIS352 4.4 14.1 1.0
O4 D:NHC1 4.5 18.4 0.4
C1 D:NHC1 4.5 12.6 0.4
C1 D:NHC1 4.6 20.1 0.4
C5 D:NHC1 4.7 20.2 0.4
NE2 D:HIS304 4.7 21.3 1.0
C10 D:NHC1 4.7 13.9 0.4
OD1 D:ASN303 4.8 21.4 1.0
CE1 D:PHE446 4.8 21.8 1.0
CA D:HIS427 4.8 18.1 1.0
O D:HIS427 5.0 18.0 1.0
C7 D:NHC1 5.0 14.0 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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