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Magnesium in PDB 5siy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5siy was solved by C.Joseph, J.Benz, A.Flohr, L.Gobbi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.41 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.911, 134.911, 236.562, 90, 90, 120
R / Rfree (%) 17.5 / 22.1

Other elements in 5siy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine (pdb code 5siy). 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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine, PDB code: 5siy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5siy

Go back to Magnesium Binding Sites List in 5siy
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.4
occ:1.00
 OD1 A:ASP564 2.0 24.4 1.0
O A:HOH982 2.0 27.1 1.0
O A:HOH937 2.0 25.0 1.0
O A:HOH918 2.1 24.2 1.0
O A:HOH933 2.2 24.8 1.0
O A:HOH963 2.2 26.1 1.0
CG A:ASP564 3.0 26.6 1.0
OD2 A:ASP564 3.4 26.5 1.0
ZN A:ZN801 3.8 31.5 1.0
O A:HOH969 3.8 40.2 1.0
OE2 A:GLU592 4.1 34.2 1.0
NE2 A:HIS595 4.1 27.3 1.0
O A:HOH988 4.3 29.4 1.0
OG1 A:THR633 4.3 28.9 1.0
CD2 A:HIS567 4.3 28.4 1.0
CD2 A:HIS563 4.3 26.2 1.0
O A:HIS563 4.3 30.0 1.0
CB A:ASP564 4.4 28.1 1.0
CD2 A:HIS595 4.4 24.8 1.0
CD2 A:HIS525 4.5 28.3 1.0
O A:THR633 4.5 27.9 1.0
OD2 A:ASP674 4.5 30.5 1.0
NE2 A:HIS567 4.5 25.4 1.0
NE2 A:HIS525 4.6 30.5 1.0
CB A:THR633 4.7 28.7 1.0
NE2 A:HIS563 4.7 26.9 1.0
CG A:GLU592 4.8 27.9 1.0
CA A:ASP564 4.8 28.0 1.0
CD A:GLU592 4.9 29.7 1.0

Magnesium binding site 2 out of 4 in 5siy

Go back to Magnesium Binding Sites List in 5siy
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.6
occ:1.00
 O B:HOH944 2.0 23.9 1.0
O B:HOH930 2.0 24.6 1.0
O B:HOH998 2.0 23.9 1.0
OD1 B:ASP564 2.1 28.2 1.0
O B:HOH955 2.1 21.3 1.0
O B:HOH935 2.1 23.7 1.0
CG B:ASP564 3.1 26.5 1.0
OD2 B:ASP564 3.3 24.8 1.0
ZN B:ZN801 3.7 30.4 1.0
NE2 B:HIS595 4.1 28.1 1.0
OE2 B:GLU592 4.1 28.3 1.0
O B:HOH978 4.1 32.6 1.0
OG1 B:THR633 4.2 25.2 1.0
O B:HOH971 4.2 31.9 1.0
CD2 B:HIS563 4.2 25.5 1.0
OD2 B:ASP674 4.3 27.4 1.0
CD2 B:HIS567 4.3 27.4 1.0
O B:HIS563 4.4 27.1 1.0
CD2 B:HIS595 4.4 27.5 1.0
O B:THR633 4.5 28.0 1.0
CB B:ASP564 4.5 24.2 1.0
NE2 B:HIS563 4.5 23.9 1.0
NE2 B:HIS567 4.5 25.5 1.0
CD2 B:HIS525 4.6 26.4 1.0
CB B:THR633 4.6 26.1 1.0
NE2 B:HIS525 4.7 33.4 1.0
CA B:ASP564 4.8 24.6 1.0
CG B:GLU592 4.8 28.4 1.0
CD B:GLU592 4.9 29.3 1.0

Magnesium binding site 3 out of 4 in 5siy

Go back to Magnesium Binding Sites List in 5siy
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.4
occ:1.00
 O C:HOH970 2.0 25.4 1.0
OD1 C:ASP564 2.1 26.1 1.0
O C:HOH937 2.1 26.9 1.0
O C:HOH948 2.1 21.8 1.0
O C:HOH1005 2.1 29.6 1.0
O C:HOH923 2.2 25.3 1.0
CG C:ASP564 3.1 26.0 1.0
OD2 C:ASP564 3.4 27.6 1.0
ZN C:ZN801 3.7 31.8 1.0
O C:HOH995 4.0 35.8 1.0
NE2 C:HIS595 4.0 28.8 1.0
OE2 C:GLU592 4.1 30.7 1.0
OG1 C:THR633 4.2 28.2 1.0
CD2 C:HIS563 4.3 25.3 1.0
O C:HOH954 4.3 32.5 1.0
CD2 C:HIS567 4.3 27.4 1.0
O C:HIS563 4.3 25.3 1.0
CD2 C:HIS595 4.4 27.8 1.0
CB C:ASP564 4.4 26.1 1.0
NE2 C:HIS567 4.5 27.0 1.0
OD2 C:ASP674 4.5 30.2 1.0
O C:THR633 4.5 27.9 1.0
CD2 C:HIS525 4.6 29.5 1.0
CB C:THR633 4.7 25.6 1.0
NE2 C:HIS563 4.7 24.4 1.0
CA C:ASP564 4.8 27.0 1.0
NE2 C:HIS525 4.8 31.9 1.0
CG C:GLU592 4.8 28.8 1.0
CD C:GLU592 4.9 32.2 1.0

Magnesium binding site 4 out of 4 in 5siy

Go back to Magnesium Binding Sites List in 5siy
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-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- [(3R)-3-Fluoropyrrolidin-1-Yl]-N-Methyl-2-(3-Methylquinoxalin-2-Yl)- N-(Oxan-4-Yl)Pyrazolo[1,5-A]Pyrimidin-7-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.1
occ:1.00
 O D:HOH927 2.0 30.1 1.0
O D:HOH962 2.0 34.9 1.0
O D:HOH912 2.1 30.1 1.0
O D:HOH938 2.1 27.8 1.0
O D:HOH917 2.2 33.6 1.0
OD1 D:ASP564 2.2 33.3 1.0
CG D:ASP564 3.1 33.7 1.0
OD2 D:ASP564 3.4 38.6 1.0
ZN D:ZN801 3.7 39.2 1.0
O D:HOH935 3.8 37.4 1.0
NE2 D:HIS595 4.1 38.7 1.0
OE2 D:GLU592 4.1 39.0 1.0
OG1 D:THR633 4.1 35.3 1.0
CD2 D:HIS563 4.2 33.2 1.0
CD2 D:HIS567 4.3 38.8 1.0
O D:HIS563 4.3 31.6 1.0
CD2 D:HIS595 4.3 35.5 1.0
O D:HOH939 4.4 42.6 1.0
OD2 D:ASP674 4.4 36.5 1.0
CB D:ASP564 4.5 34.0 1.0
NE2 D:HIS567 4.5 35.1 1.0
O D:THR633 4.6 37.8 1.0
CB D:THR633 4.6 35.2 1.0
NE2 D:HIS563 4.6 34.3 1.0
NE2 D:HIS525 4.6 42.5 1.0
CD2 D:HIS525 4.7 35.9 1.0
CA D:ASP564 4.8 33.1 1.0
CD D:GLU592 4.9 39.2 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 20:02:02 2025

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