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Zinc in PDB 3h69: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms Complexed with Endothall

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

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms Complexed with Endothall:
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 Endothall, PDB code: 3h69 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) 38.32 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.535, 41.778, 105.483, 90.00, 97.28, 90.00
R / Rfree (%) 16.2 / 22.7

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 Endothall (pdb code 3h69). 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 Endothall, PDB code: 3h69:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 3h69

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn500

b:4.7
occ:0.90
 OD1 A:ASN303 2.0 16.9 1.0
O4 A:ENL0 2.0 22.7 1.0
NE2 A:HIS352 2.0 3.9 1.0
ND1 A:HIS427 2.1 9.4 1.0
O3 A:ENL0 2.4 25.6 1.0
OD2 A:ASP271 2.6 12.3 1.0
C7 A:ENL0 2.6 27.9 1.0
CE1 A:HIS427 2.9 11.9 1.0
CD2 A:HIS352 3.0 11.4 1.0
CE1 A:HIS352 3.0 3.0 1.0
CG A:ASN303 3.1 13.8 1.0
CG A:HIS427 3.2 10.7 1.0
CG A:ASP271 3.4 12.1 1.0
ZN A:ZN501 3.5 5.4 0.9
CA A:HIS427 3.6 11.3 1.0
ND2 A:ASN303 3.7 14.7 1.0
CB A:HIS427 3.7 9.9 1.0
OD2 A:ASP242 3.8 16.5 1.0
OD1 A:ASP271 3.8 8.7 1.0
C2 A:ENL0 4.0 35.4 1.0
C3 A:ENL0 4.1 29.9 1.0
NE2 A:HIS427 4.1 14.5 1.0
ND1 A:HIS352 4.1 12.6 1.0
CG A:HIS352 4.2 10.3 1.0
O1 A:ENL0 4.2 30.1 1.0
O A:HIS427 4.2 14.8 1.0
CD2 A:HIS427 4.3 8.7 1.0
CB A:ASN303 4.3 12.9 1.0
N A:ASN303 4.3 11.8 1.0
C A:HIS427 4.4 11.4 1.0
O A:LEU385 4.4 11.0 1.0
O2 A:ENL0 4.6 28.1 0.5
CB A:ASP271 4.6 12.2 1.0
N A:HIS427 4.6 9.7 1.0
CD2 A:HIS304 4.8 14.0 1.0
CG A:ASP242 4.8 15.5 1.0
O2 A:ENL0 4.8 30.8 0.5
CA A:ASN303 4.9 14.2 1.0
C8 A:ENL0 4.9 32.4 0.5
OD1 A:ASP242 5.0 16.3 1.0

Zinc binding site 2 out of 4 in 3h69

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:5.4
occ:0.90
 O2 A:ENL0 1.8 28.1 0.5
O2 A:ENL0 1.9 30.8 0.5
OD2 A:ASP242 2.0 16.5 1.0
OD2 A:ASP271 2.1 12.3 1.0
NE2 A:HIS244 2.2 15.0 1.0
O4 A:ENL0 2.3 22.7 1.0
O1 A:ENL0 2.5 30.1 1.0
C8 A:ENL0 2.8 32.4 0.5
C8 A:ENL0 2.9 27.9 0.5
C7 A:ENL0 2.9 27.9 1.0
CE1 A:HIS244 3.1 8.9 1.0
CG A:ASP271 3.1 12.1 1.0
CD2 A:HIS244 3.2 11.0 1.0
CG A:ASP242 3.2 15.5 1.0
C6 A:ENL0 3.3 35.1 1.0
C4 A:ENL0 3.4 30.6 1.0
C2 A:ENL0 3.5 35.4 1.0
ZN A:ZN500 3.5 4.7 0.9
C3 A:ENL0 3.5 29.9 1.0
CB A:ASP271 3.7 12.2 1.0
O5 A:ENL0 3.7 28.7 0.5
O3 A:ENL0 3.9 25.6 1.0
CB A:ASP242 3.9 15.4 1.0
O5 A:ENL0 3.9 24.5 0.5
OD1 A:ASP271 4.2 8.7 1.0
OD1 A:ASP242 4.2 16.3 1.0
ND1 A:HIS244 4.2 10.1 1.0
CD2 A:HIS304 4.2 14.0 1.0
CG A:HIS244 4.3 12.7 1.0
CE1 A:HIS352 4.5 3.0 1.0
NE2 A:HIS352 4.5 3.9 1.0
C5 A:ENL0 4.6 34.3 1.0
NE2 A:HIS304 4.7 15.3 1.0
OD1 A:ASN303 4.7 16.9 1.0
C1 A:ENL0 4.8 40.2 1.0
CA A:HIS427 4.8 11.3 1.0
CE1 A:PHE446 4.9 20.1 1.0

Zinc binding site 3 out of 4 in 3h69

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn500

b:7.1
occ:0.90
 OD1 D:ASN303 2.0 21.4 1.0
NE2 D:HIS352 2.1 12.4 1.0
O4 D:ENL0 2.1 35.5 1.0
O3 D:ENL0 2.1 38.3 1.0
ND1 D:HIS427 2.1 16.7 1.0
C7 D:ENL0 2.4 37.1 1.0
OD2 D:ASP271 2.6 17.1 1.0
CE1 D:HIS352 3.0 16.8 1.0
CE1 D:HIS427 3.0 18.9 1.0
CG D:ASN303 3.1 20.9 1.0
CD2 D:HIS352 3.1 22.9 1.0
CG D:HIS427 3.2 12.9 1.0
CG D:ASP271 3.4 20.6 1.0
ZN D:ZN501 3.4 7.2 0.9
ND2 D:ASN303 3.5 14.9 1.0
CA D:HIS427 3.5 14.7 1.0
CB D:HIS427 3.6 15.8 1.0
OD1 D:ASP271 3.6 18.2 1.0
C3 D:ENL0 3.8 40.8 1.0
OD2 D:ASP242 3.8 19.5 1.0
C2 D:ENL0 3.9 44.6 1.0
ND1 D:HIS352 4.1 13.7 1.0
NE2 D:HIS427 4.2 18.2 1.0
O D:HIS427 4.2 18.0 1.0
CG D:HIS352 4.2 15.8 1.0
CD2 D:HIS427 4.3 11.6 1.0
O1 D:ENL0 4.3 39.7 1.0
CB D:ASN303 4.4 18.8 1.0
C D:HIS427 4.4 16.9 1.0
N D:ASN303 4.5 19.4 1.0
N D:HIS427 4.5 17.0 1.0
O D:LEU385 4.5 19.8 1.0
O2 D:ENL0 4.6 36.8 0.5
CB D:ASP271 4.6 17.5 1.0
CD2 D:HIS304 4.6 24.7 1.0
O2 D:ENL0 4.7 31.4 0.5
CG D:ASP242 4.8 21.1 1.0
C4 D:ENL0 4.9 41.2 1.0
CA D:ASN303 5.0 20.5 1.0
C8 D:ENL0 5.0 36.1 0.5

Zinc binding site 4 out of 4 in 3h69

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:7.2
occ:0.90
 O2 D:ENL0 2.0 36.8 0.5
OD2 D:ASP271 2.1 17.1 1.0
O2 D:ENL0 2.1 31.4 0.5
NE2 D:HIS244 2.2 9.0 1.0
OD2 D:ASP242 2.3 19.5 1.0
O4 D:ENL0 2.4 35.5 1.0
O1 D:ENL0 2.6 39.7 1.0
C7 D:ENL0 3.0 37.1 1.0
C8 D:ENL0 3.0 40.5 0.5
CG D:ASP271 3.1 20.6 1.0
C8 D:ENL0 3.1 36.1 0.5
CE1 D:HIS244 3.1 11.6 1.0
CD2 D:HIS244 3.2 11.3 1.0
CG D:ASP242 3.3 21.1 1.0
ZN D:ZN500 3.4 7.1 0.9
C2 D:ENL0 3.4 44.6 1.0
C6 D:ENL0 3.5 44.7 1.0
CB D:ASP271 3.5 17.5 1.0
C3 D:ENL0 3.5 40.8 1.0
C4 D:ENL0 3.6 41.2 1.0
O3 D:ENL0 3.7 38.3 1.0
CB D:ASP242 3.8 22.2 1.0
O5 D:ENL0 4.0 39.4 0.5
O5 D:ENL0 4.1 28.2 0.5
CD2 D:HIS304 4.1 24.7 1.0
OD1 D:ASP271 4.2 18.2 1.0
ND1 D:HIS244 4.2 14.6 1.0
CG D:HIS244 4.3 16.8 1.0
OD1 D:ASP242 4.4 23.7 1.0
CE1 D:HIS352 4.4 16.8 1.0
NE2 D:HIS352 4.4 12.4 1.0
NE2 D:HIS304 4.6 21.3 1.0
CA D:HIS427 4.7 14.7 1.0
CE1 D:PHE446 4.8 19.8 1.0
OD1 D:ASN303 4.8 21.4 1.0
C1 D:ENL0 4.8 47.7 1.0
C5 D:ENL0 4.8 48.0 1.0
CA D:ASP271 5.0 17.4 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: Thu Oct 24 14:15:51 2024

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