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Magnesium in PDB 5sjm: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One, PDB code: 5sjm was solved by C.Joseph, J.Benz, A.Flohr, K.Bleicher, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.22 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.799, 134.799, 232.623, 90, 90, 120
R / Rfree (%) 18.4 / 24.2

Other elements in 5sjm:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One 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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One (pdb code 5sjm). 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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One, PDB code: 5sjm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjm

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.7
occ:1.00
 O A:HOH967 1.8 31.7 1.0
O A:HOH904 1.9 24.3 1.0
O A:HOH929 2.0 26.6 1.0
OD1 A:ASP564 2.0 32.0 1.0
O A:HOH915 2.0 30.0 1.0
O A:HOH931 2.2 25.6 1.0
CG A:ASP564 3.0 32.2 1.0
OD2 A:ASP564 3.4 36.2 1.0
O A:HOH957 3.5 48.4 1.0
ZN A:ZN801 3.8 37.9 1.0
OE2 A:GLU592 4.0 40.9 1.0
NE2 A:HIS595 4.1 33.0 1.0
CD2 A:HIS567 4.1 34.0 1.0
O A:HOH916 4.3 45.4 1.0
NE2 A:HIS567 4.3 36.2 1.0
OG1 A:THR633 4.4 37.8 1.0
CB A:ASP564 4.4 28.2 1.0
CD2 A:HIS563 4.4 31.0 1.0
CD2 A:HIS595 4.4 35.1 1.0
O A:HIS563 4.4 31.1 1.0
OD2 A:ASP674 4.5 45.3 1.0
CD2 A:HIS525 4.6 34.4 1.0
O A:THR633 4.6 38.7 1.0
NE2 A:HIS525 4.6 35.3 1.0
NE2 A:HIS563 4.7 28.8 1.0
CA A:ASP564 4.8 31.4 1.0
CB A:THR633 4.8 36.0 1.0
CD A:GLU592 4.9 42.2 1.0
CG A:GLU592 5.0 35.6 1.0

Magnesium binding site 2 out of 4 in 5sjm

Go back to Magnesium Binding Sites List in 5sjm
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.4
occ:1.00
 O B:HOH913 1.9 29.3 1.0
O B:HOH931 2.0 25.2 1.0
O B:HOH921 2.0 20.4 1.0
O B:HOH947 2.0 24.6 1.0
O B:HOH902 2.1 29.9 1.0
OD1 B:ASP564 2.2 30.9 1.0
CG B:ASP564 3.2 30.0 1.0
OD2 B:ASP564 3.6 33.0 1.0
OE2 B:GLU592 3.8 39.1 1.0
O B:HOH934 3.8 36.7 1.0
O B:HOH942 3.9 45.2 1.0
ZN B:ZN801 4.0 34.9 1.0
NE2 B:HIS595 4.0 38.7 1.0
CD2 B:HIS567 4.3 36.6 1.0
OG1 B:THR633 4.3 33.9 1.0
CD2 B:HIS595 4.3 40.9 1.0
OD2 B:ASP674 4.4 36.1 1.0
CD2 B:HIS563 4.4 26.4 1.0
O B:HIS563 4.4 34.5 1.0
NE2 B:HIS567 4.4 35.4 1.0
O B:THR633 4.5 33.3 1.0
CB B:ASP564 4.5 28.3 1.0
CD B:GLU592 4.6 36.6 1.0
NE2 B:HIS563 4.7 27.9 1.0
NE2 B:HIS525 4.7 34.1 1.0
CD2 B:HIS525 4.7 34.3 1.0
CB B:THR633 4.7 35.7 1.0
CG B:GLU592 4.8 38.4 1.0
CA B:ASP564 4.8 31.4 1.0
O B:HOH961 4.9 37.5 1.0

Magnesium binding site 3 out of 4 in 5sjm

Go back to Magnesium Binding Sites List in 5sjm
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.3
occ:1.00
 OD1 C:ASP564 1.9 31.6 1.0
O C:HOH935 2.0 31.7 1.0
O C:HOH918 2.0 27.0 1.0
O C:HOH926 2.0 32.0 1.0
O C:HOH942 2.1 28.0 1.0
O C:HOH965 2.1 30.8 1.0
CG C:ASP564 2.9 29.2 1.0
OD2 C:ASP564 3.3 31.8 1.0
ZN C:ZN801 3.7 37.1 1.0
NE2 C:HIS595 3.9 34.4 1.0
CD2 C:HIS563 4.1 27.4 1.0
OE2 C:GLU592 4.1 35.8 1.0
O C:HIS563 4.2 28.6 1.0
CD2 C:HIS567 4.2 34.8 1.0
OG1 C:THR633 4.2 33.8 1.0
CD2 C:HIS595 4.3 33.0 1.0
CB C:ASP564 4.3 26.8 1.0
OD2 C:ASP674 4.4 37.8 1.0
NE2 C:HIS563 4.4 28.3 1.0
NE2 C:HIS567 4.5 38.9 1.0
O C:HOH960 4.5 43.7 1.0
O C:THR633 4.6 35.4 1.0
CA C:ASP564 4.6 29.6 1.0
NE2 C:HIS525 4.7 45.0 1.0
CB C:THR633 4.7 33.5 1.0
CD2 C:HIS525 4.7 41.7 1.0
CG C:GLU592 4.9 34.8 1.0
CD C:GLU592 4.9 36.4 1.0
C C:HIS563 5.0 28.4 1.0
CE1 C:HIS595 5.0 34.3 1.0

Magnesium binding site 4 out of 4 in 5sjm

Go back to Magnesium Binding Sites List in 5sjm
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:51.0
occ:1.00
 O D:HOH907 2.0 48.7 1.0
O D:HOH911 2.0 36.0 1.0
OD1 D:ASP564 2.1 55.0 1.0
O D:HOH921 2.1 42.7 1.0
O D:HOH920 2.1 50.2 1.0
O D:HOH905 2.2 53.9 1.0
CG D:ASP564 3.0 48.8 1.0
OD2 D:ASP564 3.3 58.1 1.0
O D:HOH914 3.7 35.4 1.0
ZN D:ZN801 3.8 56.0 1.0
NE2 D:HIS595 3.9 50.3 1.0
OE2 D:GLU592 3.9 61.9 1.0
CD2 D:HIS567 4.1 44.0 1.0
O D:HIS563 4.2 45.9 1.0
CD2 D:HIS595 4.3 50.1 1.0
CD2 D:HIS563 4.3 44.2 1.0
NE2 D:HIS567 4.3 43.6 1.0
CB D:ASP564 4.4 46.1 1.0
OG1 D:THR633 4.4 51.9 1.0
O D:THR633 4.5 58.9 1.0
OD2 D:ASP674 4.6 61.4 1.0
CD2 D:HIS525 4.7 55.0 1.0
NE2 D:HIS563 4.7 41.4 1.0
CA D:ASP564 4.7 45.8 1.0
NE2 D:HIS525 4.8 60.1 1.0
CD D:GLU592 4.8 54.4 1.0
CB D:THR633 4.9 49.2 1.0
CE1 D:HIS595 4.9 53.4 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 20:08:34 2025

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