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Magnesium in PDB 5sin: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide, PDB code: 5sin was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 2.40
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.881, 135.881, 234.971, 90, 90, 120
R / Rfree (%) 19.3 / 26.2

Other elements in 5sin:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide 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 N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide (pdb code 5sin). 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-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide, PDB code: 5sin:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sin

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide


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-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.1
occ:1.00
 O A:HOH925 1.8 32.0 1.0
O A:HOH952 1.9 44.2 1.0
O A:HOH903 1.9 25.1 1.0
OD1 A:ASP564 2.0 39.6 1.0
O A:HOH937 2.1 35.8 1.0
O A:HOH916 2.2 31.1 1.0
CG A:ASP564 2.9 36.4 1.0
OD2 A:ASP564 3.1 38.3 1.0
ZN A:ZN801 3.8 39.0 1.0
O A:HOH930 4.0 40.1 1.0
O A:HOH953 4.0 41.7 1.0
NE2 A:HIS595 4.2 31.0 1.0
CD2 A:HIS567 4.2 43.5 1.0
OE2 A:GLU592 4.2 42.7 1.0
CB A:ASP564 4.3 30.7 1.0
NE2 A:HIS567 4.3 44.7 1.0
CD2 A:HIS563 4.4 28.9 1.0
OG1 A:THR633 4.5 33.6 1.0
O A:HIS563 4.5 30.3 1.0
CD2 A:HIS525 4.5 38.0 1.0
O A:THR633 4.5 36.0 1.0
NE2 A:HIS525 4.6 35.0 1.0
CD2 A:HIS595 4.6 32.4 1.0
OD2 A:ASP674 4.6 48.8 1.0
NE2 A:HIS563 4.7 26.0 1.0
CA A:ASP564 4.8 29.9 1.0
CB A:THR633 4.9 35.6 1.0

Magnesium binding site 2 out of 4 in 5sin

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide


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-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.5
occ:1.00
 O B:HOH914 1.9 30.0 1.0
O B:HOH963 1.9 28.9 1.0
O B:HOH923 1.9 29.2 1.0
O B:HOH954 1.9 25.9 1.0
O B:HOH934 2.0 18.9 1.0
OD1 B:ASP564 2.2 24.6 1.0
CG B:ASP564 3.2 26.9 1.0
OD2 B:ASP564 3.5 29.8 1.0
O B:HOH944 3.8 43.0 1.0
OE2 B:GLU592 3.9 34.8 1.0
ZN B:ZN801 3.9 33.6 1.0
NE2 B:HIS595 4.2 33.3 1.0
O B:HOH965 4.2 34.7 1.0
OG1 B:THR633 4.2 31.9 1.0
O B:HIS563 4.3 32.5 1.0
CD2 B:HIS567 4.4 38.9 1.0
NE2 B:HIS567 4.4 40.8 1.0
CD2 B:HIS595 4.4 35.9 1.0
CD2 B:HIS563 4.4 21.2 1.0
OD2 B:ASP674 4.5 32.0 1.0
O B:THR633 4.5 30.5 1.0
CB B:ASP564 4.5 26.1 1.0
CD2 B:HIS525 4.6 38.9 1.0
NE2 B:HIS525 4.7 37.1 1.0
CB B:THR633 4.8 38.0 1.0
CD B:GLU592 4.8 35.6 1.0
NE2 B:HIS563 4.8 21.0 1.0
CA B:ASP564 4.9 28.7 1.0
CG B:GLU592 4.9 33.6 1.0
O B:HOH947 5.0 44.5 1.0

Magnesium binding site 3 out of 4 in 5sin

Go back to Magnesium Binding Sites List in 5sin
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide


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-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.9
occ:1.00
 O C:HOH919 1.8 24.6 1.0
O C:HOH917 2.0 29.7 1.0
OD1 C:ASP564 2.1 33.5 1.0
O C:HOH940 2.1 30.3 1.0
O C:HOH945 2.1 29.6 1.0
O C:HOH913 2.2 22.8 1.0
CG C:ASP564 3.2 30.4 1.0
OD2 C:ASP564 3.6 30.5 1.0
ZN C:ZN801 3.9 34.9 1.0
CD2 C:HIS567 3.9 41.4 1.0
OE2 C:GLU592 4.0 38.5 1.0
NE2 C:HIS595 4.1 34.5 1.0
NE2 C:HIS567 4.1 43.4 1.0
CD2 C:HIS563 4.3 25.9 1.0
O C:HIS563 4.3 32.6 1.0
OD2 C:ASP674 4.4 47.4 1.0
CD2 C:HIS595 4.5 34.3 1.0
CD2 C:HIS525 4.5 46.1 1.0
CB C:ASP564 4.5 28.1 1.0
OG1 C:THR633 4.5 30.4 1.0
NE2 C:HIS525 4.5 48.0 1.0
O C:THR633 4.6 28.1 1.0
NE2 C:HIS563 4.6 28.4 1.0
CA C:ASP564 4.8 29.7 1.0
CD C:GLU592 4.8 41.8 1.0
CG C:GLU592 4.9 36.1 1.0
CB C:THR633 5.0 29.8 1.0

Magnesium binding site 4 out of 4 in 5sin

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide


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-(3- Methyl-1-Pyridin-2-Ylthieno[2,3-C]Pyrazol-5-Yl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:41.7
occ:1.00
 O D:HOH907 1.8 43.8 1.0
O D:HOH911 1.9 36.0 1.0
O D:HOH913 1.9 35.2 1.0
O D:HOH904 1.9 33.5 1.0
O D:HOH924 2.0 47.9 1.0
OD1 D:ASP564 2.2 44.5 1.0
CG D:ASP564 2.9 47.1 1.0
OD2 D:ASP564 3.1 52.3 1.0
O D:HOH925 3.5 42.0 1.0
ZN D:ZN801 3.7 47.1 1.0
CD2 D:HIS563 4.1 34.8 1.0
OE2 D:GLU592 4.1 55.2 1.0
NE2 D:HIS595 4.2 41.5 1.0
OG1 D:THR633 4.3 36.4 1.0
CB D:ASP564 4.3 45.6 1.0
O D:THR633 4.3 45.7 1.0
NE2 D:HIS563 4.4 35.2 1.0
CD2 D:HIS525 4.4 45.9 1.0
O D:HIS563 4.4 40.6 1.0
CD2 D:HIS567 4.4 48.0 1.0
OD2 D:ASP674 4.5 56.7 1.0
NE2 D:HIS525 4.6 48.0 1.0
CD2 D:HIS595 4.6 38.8 1.0
CB D:THR633 4.6 41.1 1.0
NE2 D:HIS567 4.7 47.1 1.0
CA D:ASP564 4.7 42.7 1.0
OD1 D:ASP674 4.9 57.3 1.0
CG D:GLU592 5.0 44.6 1.0
CD D:GLU592 5.0 50.0 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 19:59:14 2025

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