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Magnesium in PDB 5sik: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine, PDB code: 5sik was solved by C.Joseph, J.Benz, A.Flohr, M.Boehringer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.86 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.91, 134.91, 233.758, 90, 90, 120
R / Rfree (%) 18.3 / 22.2

Other elements in 5sik:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine (pdb code 5sik). 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 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine, PDB code: 5sik:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sik

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-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 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.5
occ:1.00
 O A:HOH1000 1.9 29.9 1.0
O A:HOH944 2.0 29.2 1.0
OD1 A:ASP564 2.1 28.2 1.0
O A:HOH926 2.1 30.6 1.0
O A:HOH958 2.1 26.9 1.0
O A:HOH943 2.2 29.5 1.0
CG A:ASP564 3.1 29.2 1.0
OD2 A:ASP564 3.4 32.2 1.0
ZN A:ZN801 3.8 35.1 1.0
O A:HOH975 3.9 35.5 1.0
OE2 A:GLU592 4.1 34.9 1.0
NE2 A:HIS595 4.1 32.2 1.0
O A:HOH961 4.2 41.7 1.0
CD2 A:HIS567 4.2 37.0 1.0
OG1 A:THR633 4.2 34.3 1.0
CD2 A:HIS563 4.2 27.4 1.0
NE2 A:HIS567 4.4 36.1 1.0
CD2 A:HIS595 4.4 29.8 1.0
O A:HIS563 4.4 29.8 1.0
OD2 A:ASP674 4.4 37.0 1.0
CB A:ASP564 4.4 29.1 1.0
O A:THR633 4.5 32.9 1.0
NE2 A:HIS563 4.6 29.1 1.0
CD2 A:HIS525 4.6 35.1 1.0
CB A:THR633 4.7 33.6 1.0
NE2 A:HIS525 4.7 36.7 1.0
CA A:ASP564 4.8 29.9 1.0
CD A:GLU592 4.9 35.4 1.0
CG A:GLU592 4.9 33.4 1.0

Magnesium binding site 2 out of 4 in 5sik

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-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 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.1
occ:1.00
 O B:HOH932 1.9 26.5 1.0
O B:HOH948 2.0 29.2 1.0
O B:HOH990 2.0 27.8 1.0
O B:HOH964 2.1 24.9 1.0
OD1 B:ASP564 2.1 32.0 1.0
O B:HOH930 2.1 26.3 1.0
CG B:ASP564 3.1 30.7 1.0
OD2 B:ASP564 3.4 30.6 1.0
ZN B:ZN801 3.8 34.7 1.0
O B:HOH996 3.9 53.0 1.0
O B:HOH973 3.9 46.1 1.0
NE2 B:HIS595 4.0 34.4 1.0
OE2 B:GLU592 4.0 36.8 1.0
CD2 B:HIS567 4.2 32.3 1.0
O B:HOH965 4.2 40.3 1.0
CD2 B:HIS563 4.2 28.3 1.0
CD2 B:HIS595 4.2 34.7 1.0
OG1 B:THR633 4.3 31.8 1.0
NE2 B:HIS567 4.4 32.3 1.0
O B:HIS563 4.4 35.1 1.0
OD2 B:ASP674 4.4 34.8 1.0
CB B:ASP564 4.5 30.2 1.0
NE2 B:HIS563 4.6 27.7 1.0
O B:THR633 4.6 32.0 1.0
CD2 B:HIS525 4.6 34.1 1.0
CA B:ASP564 4.7 30.8 1.0
CB B:THR633 4.7 32.4 1.0
CG B:GLU592 4.8 33.8 1.0
NE2 B:HIS525 4.8 37.8 1.0
CD B:GLU592 4.8 33.8 1.0

Magnesium binding site 3 out of 4 in 5sik

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-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 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.8
occ:1.00
 O C:HOH981 2.0 31.9 1.0
O C:HOH996 2.0 29.4 1.0
O C:HOH921 2.1 31.4 1.0
O C:HOH924 2.1 27.4 1.0
OD1 C:ASP564 2.1 28.9 1.0
O C:HOH935 2.2 30.1 1.0
CG C:ASP564 3.2 29.8 1.0
OD2 C:ASP564 3.6 30.5 1.0
ZN C:ZN801 3.8 35.1 1.0
O C:HOH976 3.9 37.0 1.0
OE2 C:GLU592 4.1 36.8 1.0
NE2 C:HIS595 4.1 32.8 1.0
CD2 C:HIS567 4.1 37.5 1.0
OG1 C:THR633 4.1 33.1 1.0
CD2 C:HIS563 4.2 27.0 1.0
O C:HOH965 4.2 41.0 1.0
O C:HIS563 4.3 30.4 1.0
OD2 C:ASP674 4.3 36.3 1.0
CD2 C:HIS595 4.3 30.9 1.0
NE2 C:HIS567 4.4 37.1 1.0
O C:THR633 4.5 32.6 1.0
NE2 C:HIS563 4.5 28.1 1.0
CB C:ASP564 4.5 29.1 1.0
CB C:THR633 4.6 31.6 1.0
CG C:GLU592 4.8 33.1 1.0
CA C:ASP564 4.8 30.0 1.0
CD2 C:HIS525 4.8 37.5 1.0
CD C:GLU592 4.9 35.7 1.0
NE2 C:HIS525 4.9 41.5 1.0

Magnesium binding site 4 out of 4 in 5sik

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- (Cyclopentylmethoxy)Pyrimidin-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 5- (Cyclopentylmethoxy)Pyrimidin-2-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:43.2
occ:1.00
 O D:HOH932 2.1 40.3 1.0
OD1 D:ASP564 2.1 42.5 1.0
O D:HOH911 2.1 41.5 1.0
O D:HOH910 2.1 42.6 1.0
O D:HOH942 2.1 37.2 1.0
O D:HOH919 2.2 34.4 1.0
CG D:ASP564 3.1 42.1 1.0
OD2 D:ASP564 3.4 45.0 1.0
ZN D:ZN801 3.8 47.0 1.0
O D:HOH941 3.9 44.9 1.0
O D:HOH945 4.0 44.1 1.0
OE2 D:GLU592 4.0 48.3 1.0
NE2 D:HIS595 4.1 44.4 1.0
CD2 D:HIS567 4.1 48.4 1.0
OG1 D:THR633 4.2 41.5 1.0
CD2 D:HIS595 4.3 44.3 1.0
NE2 D:HIS567 4.4 46.9 1.0
CD2 D:HIS563 4.4 37.8 1.0
O D:HIS563 4.4 41.7 1.0
CB D:ASP564 4.4 43.9 1.0
OD2 D:ASP674 4.5 46.7 1.0
O D:THR633 4.6 50.4 1.0
CB D:THR633 4.6 45.4 1.0
CD2 D:HIS525 4.8 52.0 1.0
CA D:ASP564 4.8 40.0 1.0
NE2 D:HIS563 4.8 37.7 1.0
CD D:GLU592 4.9 48.8 1.0
NE2 D:HIS525 4.9 55.2 1.0
CG D:GLU592 4.9 49.1 1.0
O D:HOH944 5.0 47.8 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 19:59:09 2025

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