Manganese in PDB 3h60: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms:
3.1.3.16;

The structure of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms, PDB code: 3h60 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)	65.80 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	154.414, 41.755, 105.432, 90.00, 97.07, 90.00
R / Rfree (%)	16.1 / 21.9

The binding sites of Manganese atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms (pdb code 3h60). 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, PDB code: 3h60:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn500 b:3.9 occ:1.00 NE2 A:HIS352 1.9 7.9 1.0 OD1 A:ASN303 2.0 14.4 1.0 ND1 A:HIS427 2.2 10.0 1.0 OD2 A:ASP271 2.4 9.7 1.0 CE1 A:HIS352 2.8 9.5 1.0 CD2 A:HIS352 3.0 7.0 1.0 CE1 A:HIS427 3.1 13.2 1.0 CG A:ASN303 3.1 11.6 1.0 CG A:ASP271 3.2 13.4 1.0 CG A:HIS427 3.3 10.9 1.0 MN A:MN501 3.4 7.2 0.9 OD1 A:ASP271 3.5 9.2 1.0 O A:HOH3 3.6 15.1 1.0 CA A:HIS427 3.6 12.8 1.0 ND2 A:ASN303 3.7 14.9 1.0 CB A:HIS427 3.7 11.1 1.0 ND1 A:HIS352 3.9 9.5 1.0 OD2 A:ASP242 4.0 12.0 1.0 O A:HIS427 4.0 17.1 1.0 CG A:HIS352 4.1 9.5 1.0 NE2 A:HIS427 4.3 8.6 1.0 C A:HIS427 4.3 14.5 1.0 CB A:ASN303 4.4 12.4 1.0 CD2 A:HIS427 4.4 10.6 1.0 CD2 A:HIS304 4.4 14.5 1.0 N A:ASN303 4.4 13.2 1.0 CB A:ASP271 4.5 12.1 1.0 O A:LEU385 4.5 14.3 1.0 N A:HIS427 4.7 12.3 1.0 CG A:ASP242 4.9 13.7 1.0 CA A:ASN303 4.9 13.0 1.0

Manganese binding site 2 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn501 b:7.2 occ:0.90 OD2 A:ASP242 2.0 12.0 1.0 OD2 A:ASP271 2.1 9.7 1.0 NE2 A:HIS244 2.2 12.7 1.0 O A:HOH21 2.2 13.5 1.0 CG A:ASP271 3.1 13.4 1.0 CG A:ASP242 3.1 13.7 1.0 CE1 A:HIS244 3.1 15.1 1.0 CD2 A:HIS244 3.2 13.2 1.0 MN A:MN500 3.4 3.9 1.0 CB A:ASP271 3.5 12.1 1.0 O A:HOH3 3.6 15.1 1.0 CB A:ASP242 3.8 14.5 1.0 OD1 A:ASP242 4.1 13.0 1.0 CE1 A:HIS352 4.2 9.5 1.0 OD1 A:ASP271 4.2 9.2 1.0 O A:HOH553 4.2 38.5 1.0 O A:HIS427 4.2 17.1 1.0 ND1 A:HIS244 4.3 16.4 1.0 CG A:HIS244 4.3 11.9 1.0 CD2 A:HIS304 4.3 14.5 1.0 NE2 A:HIS352 4.4 7.9 1.0 OH A:TYR451 4.4 26.1 1.0 NH1 A:ARG275 4.5 29.7 1.0 CA A:HIS427 4.5 12.8 1.0 CE1 A:PHE446 4.6 15.8 1.0 C A:HIS427 4.7 14.5 1.0 NE2 A:HIS304 4.8 16.3 1.0 OD1 A:ASN303 4.9 14.4 1.0 CA A:ASP271 4.9 12.9 1.0

Manganese binding site 3 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn500 b:5.0 occ:1.00 NE2 B:HIS352 1.9 11.5 1.0 OD1 B:ASN303 2.0 16.4 1.0 ND1 B:HIS427 2.2 12.2 1.0 OD2 B:ASP271 2.4 11.7 1.0 CE1 B:HIS352 2.7 13.3 1.0 CD2 B:HIS352 3.0 10.1 1.0 CE1 B:HIS427 3.1 18.5 1.0 CG B:ASN303 3.1 14.9 1.0 CG B:ASP271 3.1 16.1 1.0 CG B:HIS427 3.3 17.1 1.0 MN B:MN501 3.4 8.1 0.8 OD1 B:ASP271 3.4 13.9 1.0 O B:HOH1 3.4 16.5 1.0 ND2 B:ASN303 3.6 15.3 1.0 CA B:HIS427 3.6 16.3 1.0 CB B:HIS427 3.7 17.1 1.0 ND1 B:HIS352 3.9 8.6 1.0 OD2 B:ASP242 3.9 18.2 1.0 CG B:HIS352 4.0 13.3 1.0 O B:HIS427 4.0 18.1 1.0 NE2 B:HIS427 4.3 16.3 1.0 CD2 B:HIS304 4.4 19.0 1.0 C B:HIS427 4.4 17.6 1.0 CD2 B:HIS427 4.4 18.3 1.0 CB B:ASN303 4.4 16.7 1.0 N B:ASN303 4.4 18.6 1.0 CB B:ASP271 4.5 15.5 1.0 O B:LEU385 4.5 15.8 1.0 N B:HIS427 4.7 16.6 1.0 CG B:ASP242 4.9 20.1 1.0 CA B:ASN303 4.9 18.5 1.0 O B:HOH89 5.0 16.7 1.0

Manganese binding site 4 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C)with Two MN2+ Atoms


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn501 b:8.1 occ:0.80 OD2 B:ASP242 2.0 18.2 1.0 OD2 B:ASP271 2.1 11.7 1.0 O B:HOH89 2.2 16.7 1.0 NE2 B:HIS244 2.2 16.9 1.0 CG B:ASP271 3.1 16.1 1.0 CG B:ASP242 3.1 20.1 1.0 CE1 B:HIS244 3.2 18.1 1.0 CD2 B:HIS244 3.2 16.7 1.0 MN B:MN500 3.4 5.0 1.0 CB B:ASP271 3.5 15.5 1.0 O B:HOH1 3.6 16.5 1.0 CB B:ASP242 3.9 17.6 1.0 OD1 B:ASP242 4.1 17.4 1.0 CE1 B:HIS352 4.1 13.3 1.0 OD1 B:ASP271 4.2 13.9 1.0 O B:HIS427 4.3 18.1 1.0 CD2 B:HIS304 4.3 19.0 1.0 ND1 B:HIS244 4.3 18.5 1.0 CG B:HIS244 4.3 16.9 1.0 NE2 B:HIS352 4.4 11.5 1.0 OH B:TYR451 4.4 24.2 1.0 NH1 B:ARG275 4.5 37.6 1.0 CA B:HIS427 4.5 16.3 1.0 CE1 B:PHE446 4.6 21.2 1.0 C B:HIS427 4.7 17.6 1.0 NE2 B:HIS304 4.7 21.4 1.0 OD1 B:ASN303 4.9 16.4 1.0 CA B:ASP271 5.0 17.1 1.0 ND1 B:HIS427 5.0 12.2 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