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Magnesium in PDB 5skq: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine, PDB code: 5skq was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.5, 135.5, 235.07, 90, 90, 120
R / Rfree (%) 16.9 / 23.5

Other elements in 5skq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine (pdb code 5skq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine, PDB code: 5skq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skq

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.9
occ:1.00
 OD1 A:ASP564 2.0 21.6 1.0
O A:HOH912 2.0 22.7 1.0
O A:HOH993 2.0 26.6 1.0
O A:HOH1028 2.1 22.9 1.0
O A:HOH937 2.2 19.1 1.0
O A:HOH942 2.2 21.8 1.0
CG A:ASP564 3.0 24.5 1.0
OD2 A:ASP564 3.4 26.5 1.0
ZN A:ZN801 3.8 28.1 1.0
O A:HOH978 4.0 29.1 1.0
NE2 A:HIS595 4.0 22.1 1.0
OE2 A:GLU592 4.1 28.4 1.0
O A:HIS563 4.2 25.8 1.0
O A:HOH997 4.3 24.1 1.0
OG1 A:THR633 4.3 24.8 1.0
CD2 A:HIS567 4.3 24.1 1.0
CD2 A:HIS595 4.3 21.0 1.0
CD2 A:HIS563 4.4 21.6 1.0
CB A:ASP564 4.4 22.4 1.0
O A:THR633 4.5 26.7 1.0
NE2 A:HIS567 4.6 27.0 1.0
OD2 A:ASP674 4.6 27.5 1.0
NE2 A:HIS525 4.7 24.9 1.0
CD2 A:HIS525 4.7 27.4 1.0
CA A:ASP564 4.7 24.4 1.0
CB A:THR633 4.8 25.7 1.0
NE2 A:HIS563 4.8 22.9 1.0
CG A:GLU592 4.8 25.6 1.0
CD A:GLU592 4.9 30.3 1.0

Magnesium binding site 2 out of 4 in 5skq

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:16.0
occ:1.00
 O B:HOH1025 2.0 21.3 1.0
O B:HOH956 2.0 15.6 1.0
O B:HOH937 2.0 14.3 1.0
O B:HOH941 2.1 17.6 1.0
O B:HOH999 2.1 14.6 1.0
OD1 B:ASP564 2.2 21.5 1.0
CG B:ASP564 3.1 18.8 1.0
OD2 B:ASP564 3.4 21.6 1.0
ZN B:ZN801 3.7 26.6 1.0
O B:HOH966 3.9 36.4 1.0
NE2 B:HIS595 4.0 20.0 1.0
O B:HOH984 4.1 26.2 1.0
OE2 B:GLU592 4.2 21.9 1.0
OG1 B:THR633 4.2 22.2 1.0
O B:HOH1042 4.3 38.4 1.0
CD2 B:HIS563 4.3 19.7 1.0
CD2 B:HIS567 4.3 23.9 1.0
O B:HIS563 4.3 19.6 1.0
CD2 B:HIS595 4.3 20.1 1.0
NE2 B:HIS567 4.4 23.5 1.0
OD2 B:ASP674 4.4 20.9 1.0
O B:THR633 4.5 24.4 1.0
CB B:ASP564 4.5 17.9 1.0
NE2 B:HIS563 4.6 18.1 1.0
CD2 B:HIS525 4.6 22.6 1.0
NE2 B:HIS525 4.6 23.8 1.0
CB B:THR633 4.7 21.6 1.0
CA B:ASP564 4.8 18.9 1.0
CG B:GLU592 4.9 22.4 1.0
CD B:GLU592 4.9 24.7 1.0

Magnesium binding site 3 out of 4 in 5skq

Go back to Magnesium Binding Sites List in 5skq
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.0
occ:1.00
 OD1 C:ASP564 2.0 18.6 1.0
O C:HOH929 2.0 20.1 1.0
O C:HOH1036 2.1 23.7 1.0
O C:HOH955 2.1 18.7 1.0
O C:HOH979 2.1 16.3 1.0
O C:HOH991 2.2 28.7 1.0
CG C:ASP564 3.0 19.4 1.0
OD2 C:ASP564 3.5 21.3 1.0
ZN C:ZN801 3.8 28.1 1.0
O C:HOH999 3.8 36.5 1.0
O C:HOH974 3.9 46.0 1.0
OE2 C:GLU592 4.1 28.5 1.0
NE2 C:HIS595 4.1 25.3 1.0
CD2 C:HIS567 4.2 22.5 1.0
O C:HOH945 4.2 27.6 1.0
CD2 C:HIS563 4.3 21.4 1.0
CB C:ASP564 4.3 19.3 1.0
O C:HIS563 4.4 22.2 1.0
CD2 C:HIS595 4.4 21.5 1.0
OD2 C:ASP674 4.4 25.7 1.0
OG1 C:THR633 4.5 21.5 1.0
O C:THR633 4.5 20.5 1.0
NE2 C:HIS567 4.5 22.3 1.0
NE2 C:HIS525 4.7 23.9 1.0
NE2 C:HIS563 4.7 21.1 1.0
CA C:ASP564 4.7 21.3 1.0
CD2 C:HIS525 4.7 25.3 1.0
CB C:THR633 4.8 21.0 1.0
CG C:GLU592 4.9 25.0 1.0
CD C:GLU592 4.9 26.7 1.0

Magnesium binding site 4 out of 4 in 5skq

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- Ethyl-6-(4-Fluorophenyl)Sulfanyl-N-Methyl-9H-Purin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:26.8
occ:1.00
 O D:HOH969 1.9 20.1 1.0
O D:HOH973 1.9 23.2 1.0
O D:HOH940 2.0 33.7 1.0
O D:HOH923 2.1 28.0 1.0
OD1 D:ASP564 2.1 30.1 1.0
O D:HOH998 2.2 23.4 1.0
CG D:ASP564 3.2 29.5 1.0
OD2 D:ASP564 3.5 28.1 1.0
O D:HOH970 3.8 38.0 1.0
O D:HOH927 3.8 41.6 1.0
ZN D:ZN801 3.9 33.3 1.0
NE2 D:HIS595 3.9 28.6 1.0
OE2 D:GLU592 4.0 25.9 1.0
OG1 D:THR633 4.1 29.3 1.0
CD2 D:HIS595 4.2 28.1 1.0
CD2 D:HIS567 4.3 29.7 1.0
CD2 D:HIS563 4.3 25.9 1.0
O D:THR633 4.4 29.3 1.0
O D:HIS563 4.4 24.7 1.0
OD2 D:ASP674 4.5 32.7 1.0
CB D:ASP564 4.5 25.4 1.0
NE2 D:HIS525 4.5 33.3 1.0
NE2 D:HIS567 4.5 29.4 1.0
CB D:THR633 4.6 26.7 1.0
CD2 D:HIS525 4.6 31.2 1.0
NE2 D:HIS563 4.8 25.6 1.0
CG D:GLU592 4.8 36.4 1.0
CA D:ASP564 4.8 27.3 1.0
CD D:GLU592 4.8 33.7 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Tue Aug 12 20:19:27 2025

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