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Magnesium in PDB 5sgv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One:
3.1.4.17;

Protein crystallography data

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

Resolution Low / High (Å) 41.46 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.008, 135.008, 234.849, 90, 90, 120
R / Rfree (%) 18.9 / 22.4

Other elements in 5sgv:

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

Magnesium binding site 1 out of 4 in 5sgv

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.9
occ:1.00
 O A:HOH921 2.0 18.4 1.0
O A:HOH1018 2.0 24.0 1.0
O A:HOH930 2.0 20.8 1.0
OD1 A:ASP564 2.0 20.9 1.0
O A:HOH934 2.1 21.5 1.0
O A:HOH955 2.1 21.5 1.0
CG A:ASP564 3.0 22.9 1.0
OD2 A:ASP564 3.4 22.6 1.0
ZN A:ZN801 3.8 28.2 1.0
O A:HOH984 4.0 23.9 1.0
OE2 A:GLU592 4.0 27.9 1.0
NE2 A:HIS595 4.0 24.9 1.0
OG1 A:THR633 4.2 25.9 1.0
CD2 A:HIS567 4.2 25.4 1.0
CD2 A:HIS563 4.3 24.5 1.0
O A:HOH947 4.3 32.3 1.0
CD2 A:HIS595 4.3 24.5 1.0
O A:HIS563 4.3 25.2 1.0
NE2 A:HIS567 4.4 25.8 1.0
CB A:ASP564 4.4 23.7 1.0
OD2 A:ASP674 4.4 28.7 1.0
O A:THR633 4.5 26.1 1.0
CB A:THR633 4.6 25.5 1.0
NE2 A:HIS563 4.6 24.9 1.0
CD2 A:HIS525 4.7 25.2 1.0
NE2 A:HIS525 4.7 26.3 1.0
CA A:ASP564 4.8 24.0 1.0
CG A:GLU592 4.8 25.6 1.0
CD A:GLU592 4.8 28.0 1.0

Magnesium binding site 2 out of 4 in 5sgv

Go back to Magnesium Binding Sites List in 5sgv
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.2
occ:1.00
 O B:HOH945 2.0 21.9 1.0
O B:HOH941 2.0 20.9 1.0
OD1 B:ASP564 2.1 23.4 1.0
O B:HOH994 2.1 18.3 1.0
O B:HOH934 2.1 20.8 1.0
O B:HOH1001 2.2 21.2 1.0
CG B:ASP564 3.0 21.4 1.0
OD2 B:ASP564 3.3 20.8 1.0
ZN B:ZN801 3.8 26.3 1.0
O B:HOH995 4.0 24.5 1.0
NE2 B:HIS595 4.0 24.2 1.0
O B:HOH1048 4.1 52.1 1.0
OE2 B:GLU592 4.1 25.3 1.0
CD2 B:HIS563 4.2 22.7 1.0
OG1 B:THR633 4.2 24.2 1.0
O B:HIS563 4.2 25.9 1.0
CD2 B:HIS567 4.2 24.1 1.0
CD2 B:HIS595 4.3 25.3 1.0
O B:HOH1003 4.3 29.1 1.0
OD2 B:ASP674 4.3 25.4 1.0
NE2 B:HIS567 4.4 23.6 1.0
CB B:ASP564 4.4 20.8 1.0
O B:HOH926 4.4 42.2 1.0
O B:THR633 4.5 23.2 1.0
NE2 B:HIS563 4.5 21.8 1.0
CB B:THR633 4.6 24.7 1.0
CD2 B:HIS525 4.6 23.9 1.0
NE2 B:HIS525 4.7 25.0 1.0
CA B:ASP564 4.7 22.3 1.0
CG B:GLU592 4.7 23.3 1.0
CD B:GLU592 4.8 23.2 1.0

Magnesium binding site 3 out of 4 in 5sgv

Go back to Magnesium Binding Sites List in 5sgv
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.5
occ:1.00
 O C:HOH1002 2.0 22.8 1.0
O C:HOH913 2.1 21.0 1.0
OD1 C:ASP564 2.1 25.2 1.0
O C:HOH947 2.1 19.6 1.0
O C:HOH1031 2.1 24.5 1.0
O C:HOH942 2.1 23.0 1.0
CG C:ASP564 3.1 24.1 1.0
OD2 C:ASP564 3.5 22.8 1.0
ZN C:ZN801 3.8 28.5 1.0
OE2 C:GLU592 4.0 29.6 1.0
O C:HOH1003 4.1 26.7 1.0
NE2 C:HIS595 4.1 26.4 1.0
CD2 C:HIS567 4.2 26.2 1.0
OG1 C:THR633 4.2 24.6 1.0
O C:HOH996 4.2 30.2 1.0
CD2 C:HIS563 4.3 23.2 1.0
OD2 C:ASP674 4.3 28.9 1.0
O C:HIS563 4.3 25.9 1.0
CD2 C:HIS595 4.3 25.9 1.0
NE2 C:HIS567 4.3 25.9 1.0
O C:THR633 4.4 25.1 1.0
CB C:ASP564 4.4 23.9 1.0
CB C:THR633 4.6 24.1 1.0
NE2 C:HIS525 4.6 27.0 1.0
CD2 C:HIS525 4.6 27.7 1.0
NE2 C:HIS563 4.7 23.6 1.0
CG C:GLU592 4.8 25.3 1.0
CA C:ASP564 4.8 25.3 1.0
CD C:GLU592 4.8 27.3 1.0

Magnesium binding site 4 out of 4 in 5sgv

Go back to Magnesium Binding Sites List in 5sgv
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-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 1- Benzyl-3-(2-Phenylpyrazol-3-Yl)Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.3
occ:1.00
 O D:HOH975 2.0 23.8 1.0
O D:HOH990 2.1 30.8 1.0
OD1 D:ASP564 2.1 27.8 1.0
O D:HOH909 2.1 22.9 1.0
O D:HOH922 2.1 23.8 1.0
O D:HOH919 2.1 27.2 1.0
CG D:ASP564 3.1 26.1 1.0
OD2 D:ASP564 3.5 28.3 1.0
ZN D:ZN801 3.8 32.7 1.0
OE2 D:GLU592 4.0 34.4 1.0
O D:HOH970 4.1 35.4 1.0
O D:HOH982 4.1 29.4 1.0
NE2 D:HIS595 4.1 31.3 1.0
OG1 D:THR633 4.2 30.1 1.0
CD2 D:HIS567 4.2 31.9 1.0
CD2 D:HIS563 4.2 27.5 1.0
CD2 D:HIS595 4.3 30.4 1.0
O D:HIS563 4.4 27.9 1.0
OD2 D:ASP674 4.4 30.9 1.0
NE2 D:HIS567 4.4 31.1 1.0
O D:THR633 4.4 31.8 1.0
CB D:ASP564 4.5 26.6 1.0
NE2 D:HIS563 4.6 25.3 1.0
CD2 D:HIS525 4.6 31.0 1.0
NE2 D:HIS525 4.6 35.2 1.0
CB D:THR633 4.7 28.9 1.0
CA D:ASP564 4.8 26.8 1.0
O D:HOH1002 4.8 36.9 1.0
CD D:GLU592 4.8 33.2 1.0
CG D:GLU592 4.9 33.9 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 19:42:07 2025

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