Zinc in PDB 3h66: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms

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

The structure of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms, PDB code: 3h66 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 / 2.59
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.251, 41.684, 106.092, 90.00, 96.46, 90.00
R / Rfree (%)	19.9 / 29.1

The binding sites of Zinc atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms (pdb code 3h66). 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, PDB code: 3h66:
Jump to Zinc binding site number: 1; 2; 3; 4;

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn500 b:2.0 occ:1.00 OD1 A:ASN303 2.1 2.0 1.0 NE2 A:HIS352 2.2 2.0 1.0 ND1 A:HIS427 2.3 2.0 1.0 OD2 A:ASP271 2.5 2.0 1.0 CE1 A:HIS352 2.9 2.0 1.0 O A:HOH5 3.0 2.0 1.0 CE1 A:HIS427 3.0 2.0 1.0 CG A:ASP271 3.1 2.0 1.0 CG A:ASN303 3.2 2.0 1.0 ZN A:ZN501 3.2 8.4 1.0 OD1 A:ASP271 3.3 2.0 1.0 CD2 A:HIS352 3.3 2.0 1.0 CG A:HIS427 3.5 2.0 1.0 CA A:HIS427 3.7 2.0 1.0 OD2 A:ASP242 3.8 2.0 1.0 ND2 A:ASN303 3.8 2.0 1.0 CB A:HIS427 4.0 2.0 1.0 O A:HIS427 4.0 2.0 1.0 ND1 A:HIS352 4.2 2.0 1.0 NE2 A:HIS427 4.3 2.0 1.0 C A:HIS427 4.3 2.0 1.0 CG A:HIS352 4.4 2.0 1.0 CB A:ASN303 4.4 2.0 1.0 CD2 A:HIS427 4.5 2.0 1.0 CB A:ASP271 4.5 2.0 1.0 N A:ASN303 4.5 2.0 1.0 CD2 A:HIS304 4.5 2.0 1.0 NH1 A:ARG400 4.7 2.0 1.0 N A:HIS427 4.8 2.0 1.0 O A:LEU385 4.8 2.0 1.0 NE2 A:HIS244 4.9 2.0 1.0 CG A:ASP242 4.9 2.0 1.0 CA A:ASN303 5.0 2.0 1.0

Zinc binding site 2 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:8.4 occ:1.00 OD2 A:ASP242 2.0 2.0 1.0 OD2 A:ASP271 2.0 2.0 1.0 NE2 A:HIS244 2.2 2.0 1.0 CE1 A:HIS244 3.1 2.0 1.0 CG A:ASP271 3.1 2.0 1.0 CG A:ASP242 3.1 2.0 1.0 CD2 A:HIS244 3.2 2.0 1.0 ZN A:ZN500 3.2 2.0 1.0 O A:HIS427 3.8 2.0 1.0 O A:HOH5 3.8 2.0 1.0 CB A:ASP271 3.8 2.0 1.0 CB A:ASP242 4.0 2.0 1.0 OD1 A:ASP271 4.0 2.0 1.0 OD1 A:ASP242 4.1 2.0 1.0 ND1 A:HIS244 4.2 2.0 1.0 OH A:TYR451 4.3 2.0 1.0 C A:HIS427 4.3 2.0 1.0 CG A:HIS244 4.3 2.0 1.0 CE1 A:PHE446 4.4 7.2 1.0 CA A:HIS427 4.4 2.0 1.0 CE1 A:HIS352 4.5 2.0 1.0 NE2 A:HIS352 4.7 2.0 1.0 CD2 A:HIS304 4.8 2.0 1.0 CZ A:TYR451 4.9 2.0 1.0 ND1 A:HIS427 4.9 2.0 1.0 OD1 A:ASN303 5.0 2.0 1.0

Zinc binding site 3 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two ZN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn500 b:2.0 occ:1.00 OD1 B:ASN303 2.1 2.0 1.0 OD2 B:ASP271 2.1 2.0 1.0 NE2 B:HIS352 2.2 2.0 1.0 ND1 B:HIS427 2.3 2.0 1.0 CE1 B:HIS352 2.8 2.0 1.0 CG B:ASP271 3.0 2.0 1.0 ZN B:ZN501 3.0 25.3 1.0 CG B:ASN303 3.0 2.0 1.0 O B:HOH12 3.1 2.0 1.0 CE1 B:HIS427 3.2 2.0 1.0 OD1 B:ASP271 3.3 2.0 1.0 OD2 B:ASP242 3.3 2.0 1.0 ND2 B:ASN303 3.4 2.0 1.0 CG B:HIS427 3.4 2.0 1.0 CD2 B:HIS352 3.4 2.0 1.0 CA B:HIS427 3.5 2.0 1.0 CB B:HIS427 3.8 2.0 1.0 O B:HIS427 3.9 2.0 1.0 ND1 B:HIS352 4.0 2.0 1.0 C B:HIS427 4.2 2.0 1.0 NE2 B:HIS427 4.4 2.0 1.0 CG B:HIS352 4.4 2.0 1.0 CD2 B:HIS304 4.4 2.0 1.0 CG B:ASP242 4.4 2.0 1.0 CB B:ASP271 4.4 2.0 1.0 N B:HIS427 4.4 2.0 1.0 CD2 B:HIS427 4.5 2.0 1.0 CB B:ASN303 4.5 2.0 1.0 NE2 B:HIS244 4.6 2.0 1.0 N B:ASN303 4.7 2.0 1.0 NH1 B:ARG400 4.7 2.0 1.0 OD1 B:ASP242 4.8 2.0 1.0 O B:LEU385 4.9 2.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn501 b:25.3 occ:1.00 OD2 B:ASP242 1.9 2.0 1.0 OD2 B:ASP271 2.1 2.0 1.0 NE2 B:HIS244 2.2 2.0 1.0 ZN B:ZN500 3.0 2.0 1.0 CG B:ASP242 3.0 2.0 1.0 CG B:ASP271 3.1 2.0 1.0 CD2 B:HIS244 3.2 2.0 1.0 CE1 B:HIS244 3.2 2.0 1.0 O B:HOH12 3.7 2.0 1.0 CB B:ASP242 3.7 2.0 1.0 CB B:ASP271 3.9 2.0 1.0 O B:HIS427 3.9 2.0 1.0 OD1 B:ASP271 4.0 2.0 1.0 OH B:TYR451 4.2 5.0 1.0 OD1 B:ASP242 4.2 2.0 1.0 ND1 B:HIS244 4.3 2.0 1.0 CG B:HIS244 4.3 2.0 1.0 CD2 B:HIS304 4.3 2.0 1.0 CE1 B:HIS352 4.4 2.0 1.0 CA B:HIS427 4.4 2.0 1.0 C B:HIS427 4.4 2.0 1.0 CE1 B:PHE446 4.6 2.0 1.0 NE2 B:HIS352 4.7 2.0 1.0 NE2 B:HIS304 4.8 2.0 1.0 OD1 B:ASN303 4.9 2.0 1.0 ND1 B:HIS427 4.9 2.0 1.0 CZ B:TYR451 4.9 2.0 1.0

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