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Manganese in PDB 3h64: Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Endothall

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

All present enzymatic activity of Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ 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 MN2+ Atoms Complexed with Endothall, PDB code: 3h64 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) 38.38 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 154.553, 41.463, 95.614, 90.00, 96.78, 90.00
R / Rfree (%) 19 / 23.7

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 Endothall (pdb code 3h64). 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 Endothall, PDB code: 3h64:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 3h64

Go back to Manganese Binding Sites List in 3h64
Manganese binding site 1 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn500

b:2.5
occ:1.00
 O2 A:ENL0 2.0 13.6 0.8
NE2 A:HIS352 2.1 2.5 1.0
OD1 A:ASN303 2.1 10.7 1.0
ND1 A:HIS427 2.2 5.1 1.0
O4 A:ENL0 2.3 10.2 0.2
OD2 A:ASP271 2.4 6.1 1.0
O3 A:ENL0 2.7 12.9 0.2
C7 A:ENL0 2.8 13.2 0.2
C8 A:ENL0 3.0 15.4 0.8
CE1 A:HIS427 3.0 5.9 1.0
CE1 A:HIS352 3.1 4.0 1.0
CD2 A:HIS352 3.1 4.3 1.0
CG A:ASN303 3.1 9.1 1.0
O5 A:ENL0 3.2 15.1 0.8
CG A:ASP271 3.3 8.1 1.0
CG A:HIS427 3.3 4.8 1.0
MN A:MN501 3.4 2.9 1.0
OD1 A:ASP271 3.6 5.4 1.0
CA A:HIS427 3.6 7.0 1.0
ND2 A:ASN303 3.7 7.1 1.0
CB A:HIS427 3.7 6.8 1.0
O4 A:ENL0 3.9 11.0 0.8
OD2 A:ASP242 4.0 5.8 1.0
O1 A:ENL0 4.1 9.5 0.2
ND1 A:HIS352 4.2 3.6 1.0
CG A:HIS352 4.2 2.0 1.0
NE2 A:HIS427 4.2 9.9 1.0
O A:HIS427 4.3 8.2 1.0
C3 A:ENL0 4.3 12.8 0.2
CB A:ASN303 4.3 6.8 1.0
C4 A:ENL0 4.4 9.7 0.8
CD2 A:HIS427 4.4 7.9 1.0
N A:ASN303 4.4 6.4 1.0
C2 A:ENL0 4.4 12.9 0.2
C A:HIS427 4.4 7.7 1.0
CB A:ASP271 4.5 7.5 1.0
O A:LEU385 4.5 4.4 1.0
C7 A:ENL0 4.6 9.3 0.8
CD2 A:HIS304 4.6 9.2 1.0
N A:HIS427 4.7 6.0 1.0
C6 A:ENL0 4.7 12.4 0.8
O1 A:ENL0 4.8 13.4 0.8
CA A:ASN303 4.9 8.5 1.0
CG A:ASP242 4.9 10.4 1.0
C8 A:ENL0 5.0 14.5 0.2

Manganese binding site 2 out of 4 in 3h64

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn501

b:2.9
occ:1.00
 O4 A:ENL0 2.0 11.0 0.8
OD2 A:ASP242 2.1 5.8 1.0
O4 A:ENL0 2.1 10.2 0.2
NE2 A:HIS244 2.1 8.8 1.0
O2 A:ENL0 2.1 12.5 0.2
O1 A:ENL0 2.2 13.4 0.8
OD2 A:ASP271 2.2 6.1 1.0
O2 A:ENL0 2.3 13.6 0.8
O1 A:ENL0 2.5 9.5 0.2
C8 A:ENL0 2.7 14.5 0.2
C6 A:ENL0 2.8 14.5 0.2
C7 A:ENL0 3.0 9.3 0.8
C7 A:ENL0 3.0 13.2 0.2
C2 A:ENL0 3.0 10.3 0.8
C8 A:ENL0 3.0 15.4 0.8
CE1 A:HIS244 3.0 8.7 1.0
C6 A:ENL0 3.2 12.4 0.8
C4 A:ENL0 3.2 13.1 0.2
CD2 A:HIS244 3.2 7.6 1.0
CG A:ASP271 3.2 8.1 1.0
CG A:ASP242 3.2 10.4 1.0
C3 A:ENL0 3.3 11.0 0.8
C4 A:ENL0 3.4 9.7 0.8
MN A:MN500 3.4 2.5 1.0
C3 A:ENL0 3.5 12.8 0.2
CB A:ASP271 3.6 7.5 1.0
C2 A:ENL0 3.6 12.9 0.2
O5 A:ENL0 3.6 15.5 0.2
CB A:ASP242 3.9 7.9 1.0
O5 A:ENL0 4.0 15.1 0.8
O3 A:ENL0 4.0 12.9 0.2
O3 A:ENL0 4.1 14.8 0.8
ND1 A:HIS244 4.2 9.7 1.0
OD1 A:ASP242 4.2 8.0 1.0
C5 A:ENL0 4.2 14.2 0.2
CD2 A:HIS304 4.3 9.2 1.0
CG A:HIS244 4.3 7.7 1.0
OD1 A:ASP271 4.4 5.4 1.0
C1 A:ENL0 4.4 12.5 0.8
C5 A:ENL0 4.4 11.2 0.8
CE1 A:HIS352 4.5 4.0 1.0
NE2 A:HIS352 4.5 2.5 1.0
CE1 A:PHE446 4.6 8.7 1.0
C1 A:ENL0 4.7 13.1 0.2
NE2 A:HIS304 4.7 14.2 1.0
CA A:HIS427 4.8 7.0 1.0
OD1 A:ASN303 4.8 10.7 1.0

Manganese binding site 3 out of 4 in 3h64

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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 Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn500

b:9.2
occ:1.00
 OD1 D:ASN303 2.0 26.2 1.0
NE2 D:HIS352 2.1 18.9 1.0
ND1 D:HIS427 2.2 23.1 1.0
O4 D:ENL0 2.3 32.0 1.0
OD2 D:ASP271 2.4 28.0 1.0
C7 D:ENL0 2.8 37.7 1.0
O3 D:ENL0 2.8 38.8 1.0
CD2 D:HIS352 3.0 20.1 1.0
CE1 D:HIS427 3.0 24.1 1.0
CG D:ASN303 3.1 28.3 1.0
CE1 D:HIS352 3.1 16.7 1.0
CG D:ASP271 3.3 28.7 1.0
CG D:HIS427 3.3 24.3 1.0
MN D:MN501 3.5 10.1 1.0
OD1 D:ASP271 3.6 29.4 1.0
ND2 D:ASN303 3.7 28.9 1.0
CA D:HIS427 3.7 25.0 1.0
CB D:HIS427 3.8 24.2 1.0
OD2 D:ASP242 4.0 29.6 1.0
C3 D:ENL0 4.1 42.0 1.0
C2 D:ENL0 4.1 43.5 1.0
CG D:HIS352 4.2 19.3 1.0
ND1 D:HIS352 4.2 22.0 1.0
NE2 D:HIS427 4.2 23.9 1.0
O D:HIS427 4.2 25.7 1.0
CB D:ASN303 4.3 29.4 1.0
N D:ASN303 4.4 28.3 1.0
CD2 D:HIS427 4.4 23.0 1.0
C D:HIS427 4.4 26.3 1.0
O1 D:ENL0 4.4 42.6 1.0
O D:LEU385 4.5 26.1 1.0
CB D:ASP271 4.6 28.4 1.0
N D:HIS427 4.6 24.4 1.0
CD2 D:HIS304 4.8 35.0 1.0
CA D:ASN303 4.9 29.8 1.0
CG D:ASP242 4.9 31.5 1.0

Manganese binding site 4 out of 4 in 3h64

Go back to Manganese Binding Sites List in 3h64
Manganese binding site 4 out of 4 in the Catalytic Domain of Human Serine/Threonine Phosphatase 5 (PP5C) with Two MN2+ Atoms Complexed with Endothall


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 Endothall within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn501

b:10.1
occ:1.00
 OD2 D:ASP242 2.0 29.6 1.0
NE2 D:HIS244 2.1 35.3 1.0
OD2 D:ASP271 2.2 28.0 1.0
O2 D:ENL0 2.4 43.2 1.0
O4 D:ENL0 2.4 32.0 1.0
O1 D:ENL0 2.6 42.6 1.0
CE1 D:HIS244 3.0 34.3 1.0
C8 D:ENL0 3.1 44.6 1.0
CG D:ASP242 3.1 31.5 1.0
CD2 D:HIS244 3.2 35.5 1.0
CG D:ASP271 3.2 28.7 1.0
C7 D:ENL0 3.2 37.7 1.0
C6 D:ENL0 3.4 44.6 1.0
C2 D:ENL0 3.5 43.5 1.0
CB D:ASP271 3.5 28.4 1.0
MN D:MN500 3.5 9.2 1.0
C4 D:ENL0 3.5 43.0 1.0
C3 D:ENL0 3.6 42.0 1.0
CB D:ASP242 3.7 31.6 1.0
O5 D:ENL0 4.0 47.8 1.0
OD1 D:ASP242 4.1 31.0 1.0
ND1 D:HIS244 4.1 35.0 1.0
CD2 D:HIS304 4.2 35.0 1.0
CG D:HIS244 4.2 35.2 1.0
OD1 D:ASP271 4.3 29.4 1.0
O3 D:ENL0 4.3 38.8 1.0
CE1 D:HIS352 4.4 16.7 1.0
NE2 D:HIS352 4.4 18.9 1.0
CE1 D:PHE446 4.6 35.3 1.0
C5 D:ENL0 4.7 45.0 1.0
C1 D:ENL0 4.8 42.9 1.0
NE2 D:HIS304 4.8 35.7 1.0
CA D:HIS427 4.9 25.0 1.0
OD1 D:ASN303 4.9 26.2 1.0
CA D:ASP271 5.0 27.9 1.0
CA D:ASP242 5.0 32.6 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 Oct 5 16:28:13 2024

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