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Manganese in PDB 3h62: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Cantharidic Acid

Enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Cantharidic Acid

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ 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 MN2+ Atoms Complexed with Cantharidic Acid, PDB code: 3h62 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) 36.08 / 1.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.535, 41.518, 97.502, 90.00, 103.44, 90.00
R / Rfree (%) 17.6 / 20.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Cantharidic Acid (pdb code 3h62). 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 Complexed with Cantharidic Acid, PDB code: 3h62:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3h62

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


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn500

b:9.1
occ:1.00
 OD1 C:ASN303 2.0 8.7 1.0
O3 C:NHC0 2.1 13.8 0.5
O3 C:NHC0 2.2 8.8 0.5
NE2 C:HIS352 2.2 7.3 1.0
ND1 C:HIS427 2.2 6.0 1.0
OD2 C:ASP271 2.3 6.1 1.0
C9 C:NHC0 2.9 11.5 0.5
C9 C:NHC0 3.0 14.4 0.5
O5 C:NHC0 3.0 9.6 0.5
CG C:ASN303 3.1 8.6 1.0
CE1 C:HIS427 3.1 6.5 1.0
O5 C:NHC0 3.1 14.9 0.5
CD2 C:HIS352 3.1 6.2 1.0
CE1 C:HIS352 3.2 5.9 1.0
CG C:ASP271 3.2 6.6 1.0
MN C:MN501 3.3 8.9 1.0
CG C:HIS427 3.3 5.8 1.0
OD1 C:ASP271 3.6 6.8 1.0
ND2 C:ASN303 3.6 10.0 1.0
CA C:HIS427 3.7 7.6 1.0
O2 C:NHC0 3.7 11.2 0.5
O2 C:NHC0 3.8 11.3 0.5
CB C:HIS427 3.8 6.5 1.0
OD2 C:ASP242 3.9 8.6 1.0
NE2 C:HIS427 4.3 7.6 1.0
ND1 C:HIS352 4.3 6.2 1.0
CG C:HIS352 4.3 5.7 1.0
O C:HIS427 4.3 9.6 1.0
CB C:ASN303 4.4 7.9 1.0
C4 C:NHC0 4.4 12.6 0.5
C4 C:NHC0 4.4 13.8 0.5
CD2 C:HIS427 4.4 6.2 1.0
C C:HIS427 4.4 8.0 1.0
N C:ASN303 4.4 7.2 1.0
CB C:ASP271 4.5 6.1 1.0
CD2 C:HIS304 4.5 8.2 1.0
O C:LEU385 4.6 7.5 1.0
C8 C:NHC0 4.7 13.3 0.5
N C:HIS427 4.7 7.0 1.0
C8 C:NHC0 4.7 13.5 0.5
C6 C:NHC0 4.7 13.7 0.5
C6 C:NHC0 4.7 13.2 0.5
O1 C:NHC0 4.8 13.3 0.5
O1 C:NHC0 4.8 13.1 0.5
CG C:ASP242 4.9 7.4 1.0
CA C:ASN303 4.9 7.6 1.0

Manganese binding site 2 out of 4 in 3h62

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


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn501

b:8.9
occ:1.00
 O3 C:NHC0 2.1 8.8 0.5
OD2 C:ASP242 2.1 8.6 1.0
O2 C:NHC0 2.2 11.2 0.5
O2 C:NHC0 2.2 11.3 0.5
NE2 C:HIS244 2.2 9.0 1.0
OD2 C:ASP271 2.2 6.1 1.0
O1 C:NHC0 2.3 13.3 0.5
O1 C:NHC0 2.3 13.1 0.5
O3 C:NHC0 2.5 13.8 0.5
C9 C:NHC0 2.9 14.4 0.5
C9 C:NHC0 3.0 11.5 0.5
CE1 C:HIS244 3.1 10.1 1.0
C6 C:NHC0 3.1 13.7 0.5
C6 C:NHC0 3.2 13.2 0.5
C8 C:NHC0 3.2 13.3 0.5
C8 C:NHC0 3.2 13.5 0.5
CG C:ASP271 3.2 6.6 1.0
CD2 C:HIS244 3.2 9.8 1.0
C2 C:NHC0 3.2 13.1 0.5
C2 C:NHC0 3.2 13.3 0.5
CG C:ASP242 3.3 7.4 1.0
MN C:MN500 3.3 9.1 1.0
C4 C:NHC0 3.4 13.8 0.5
C4 C:NHC0 3.4 12.6 0.5
C3 C:NHC0 3.5 13.4 0.5
C3 C:NHC0 3.5 13.8 0.5
CB C:ASP271 3.5 6.1 1.0
O5 C:NHC0 3.7 14.9 0.5
O5 C:NHC0 4.0 9.6 0.5
CB C:ASP242 4.0 7.0 1.0
ND1 C:HIS244 4.2 9.9 1.0
OD1 C:ASP242 4.2 8.8 1.0
CD2 C:HIS304 4.2 8.2 1.0
O4 C:NHC0 4.3 14.3 0.5
OD1 C:ASP271 4.3 6.8 1.0
O4 C:NHC0 4.3 14.4 0.5
CG C:HIS244 4.3 9.3 1.0
NE2 C:HIS352 4.4 7.3 1.0
CE1 C:HIS352 4.4 5.9 1.0
C5 C:NHC0 4.4 13.5 0.5
C5 C:NHC0 4.5 13.3 0.5
C1 C:NHC0 4.5 13.3 0.5
C1 C:NHC0 4.5 13.1 0.5
CE1 C:PHE446 4.7 9.4 1.0
OD1 C:ASN303 4.7 8.7 1.0
CA C:HIS427 4.7 7.6 1.0
NE2 C:HIS304 4.7 9.3 1.0
C10 C:NHC0 4.9 13.6 0.5
C10 C:NHC0 4.9 12.6 0.5
CA C:ASP271 5.0 5.8 1.0

Manganese binding site 3 out of 4 in 3h62

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


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn500

b:8.0
occ:1.00
 OD1 B:ASN303 2.1 7.5 1.0
O3 B:NHC0 2.1 8.2 1.0
NE2 B:HIS352 2.1 6.0 1.0
ND1 B:HIS427 2.2 8.2 1.0
OD2 B:ASP271 2.4 6.1 1.0
C9 B:NHC0 2.9 10.6 1.0
O5 B:NHC0 3.0 13.3 1.0
CE1 B:HIS427 3.1 9.0 1.0
CE1 B:HIS352 3.1 4.9 1.0
CG B:ASN303 3.1 8.5 1.0
CD2 B:HIS352 3.1 5.3 1.0
CG B:ASP271 3.3 7.2 1.0
CG B:HIS427 3.3 7.7 1.0
MN B:MN501 3.3 8.3 1.0
ND2 B:ASN303 3.6 9.1 1.0
OD1 B:ASP271 3.6 8.5 1.0
CA B:HIS427 3.6 7.1 1.0
CB B:HIS427 3.7 7.3 1.0
O2 B:NHC0 3.9 9.8 1.0
OD2 B:ASP242 4.0 7.8 1.0
ND1 B:HIS352 4.2 4.6 1.0
CG B:HIS352 4.2 5.7 1.0
NE2 B:HIS427 4.2 8.9 1.0
O B:HIS427 4.3 8.7 1.0
C4 B:NHC0 4.4 10.3 1.0
CD2 B:HIS427 4.4 9.1 1.0
CB B:ASN303 4.4 6.7 1.0
N B:ASN303 4.4 6.2 1.0
C B:HIS427 4.4 7.6 1.0
CB B:ASP271 4.5 6.8 1.0
CD2 B:HIS304 4.6 8.9 1.0
O B:LEU385 4.6 7.6 1.0
N B:HIS427 4.7 7.2 1.0
C8 B:NHC0 4.7 10.8 1.0
C6 B:NHC0 4.8 9.9 1.0
O1 B:NHC0 4.8 7.7 1.0
CG B:ASP242 4.9 7.8 1.0
O B:HOH690 4.9 32.0 1.0
CA B:ASN303 4.9 7.0 1.0

Manganese binding site 4 out of 4 in 3h62

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


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 Complexed with Cantharidic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn501

b:8.3
occ:1.00
 OD2 B:ASP242 2.1 7.8 1.0
NE2 B:HIS244 2.2 7.9 1.0
OD2 B:ASP271 2.2 6.1 1.0
O2 B:NHC0 2.2 9.8 1.0
O3 B:NHC0 2.2 8.2 1.0
O1 B:NHC0 2.2 7.7 1.0
C9 B:NHC0 2.9 10.6 1.0
CE1 B:HIS244 3.1 6.7 1.0
C6 B:NHC0 3.1 9.9 1.0
C8 B:NHC0 3.2 10.8 1.0
CG B:ASP271 3.2 7.2 1.0
C2 B:NHC0 3.2 7.8 1.0
CD2 B:HIS244 3.2 7.1 1.0
CG B:ASP242 3.3 7.8 1.0
MN B:MN500 3.3 8.0 1.0
C4 B:NHC0 3.4 10.3 1.0
C3 B:NHC0 3.5 10.2 1.0
CB B:ASP271 3.5 6.8 1.0
O5 B:NHC0 3.8 13.3 1.0
CB B:ASP242 3.9 6.9 1.0
OD1 B:ASP242 4.2 8.3 1.0
ND1 B:HIS244 4.2 6.9 1.0
CD2 B:HIS304 4.2 8.9 1.0
CG B:HIS244 4.3 7.2 1.0
OD1 B:ASP271 4.3 8.5 1.0
O4 B:NHC0 4.3 13.7 1.0
CE1 B:HIS352 4.4 4.9 1.0
C5 B:NHC0 4.4 10.1 1.0
NE2 B:HIS352 4.4 6.0 1.0
C1 B:NHC0 4.5 10.3 1.0
CE1 B:PHE446 4.6 8.7 1.0
CA B:HIS427 4.7 7.1 1.0
NE2 B:HIS304 4.7 11.4 1.0
OD1 B:ASN303 4.8 7.5 1.0
C10 B:NHC0 4.9 11.9 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: Sat Aug 16 11:52:09 2025

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