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Magnesium in PDB 5shv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One, PDB code: 5shv was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.48 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.219, 135.219, 235.119, 90, 90, 120
R / Rfree (%) 19.8 / 23.4

Other elements in 5shv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-4-One (pdb code 5shv). 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-(6- Fluoropyridin-2-Yl)Piperidin-4-One, PDB code: 5shv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shv

Go back to Magnesium Binding Sites List in 5shv
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-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-(6- Fluoropyridin-2-Yl)Piperidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.3
occ:1.00
 O A:HOH1027 2.0 22.8 1.0
O A:HOH938 2.0 26.3 1.0
OD1 A:ASP564 2.0 21.3 1.0
O A:HOH933 2.0 19.8 1.0
O A:HOH987 2.1 21.9 1.0
O A:HOH922 2.2 24.1 1.0
CG A:ASP564 3.0 22.1 1.0
OD2 A:ASP564 3.4 23.8 1.0
ZN A:ZN801 3.8 26.9 1.0
O A:HOH1038 3.9 41.0 1.0
OE2 A:GLU592 4.0 24.1 1.0
O A:HOH1013 4.0 29.4 1.0
NE2 A:HIS595 4.1 23.5 1.0
OG1 A:THR633 4.2 25.2 1.0
CD2 A:HIS563 4.3 22.2 1.0
CD2 A:HIS567 4.3 26.4 1.0
CD2 A:HIS595 4.3 22.5 1.0
O A:HOH983 4.3 29.4 1.0
O A:HIS563 4.4 23.6 1.0
OD2 A:ASP674 4.4 30.0 1.0
CB A:ASP564 4.4 22.2 1.0
O A:THR633 4.5 24.8 1.0
NE2 A:HIS567 4.6 24.6 1.0
CD2 A:HIS525 4.6 26.0 1.0
NE2 A:HIS563 4.7 22.9 1.0
NE2 A:HIS525 4.7 26.4 1.0
CB A:THR633 4.7 24.6 1.0
CA A:ASP564 4.8 22.8 1.0
CG A:GLU592 4.8 23.4 1.0
CD A:GLU592 4.8 24.3 1.0

Magnesium binding site 2 out of 4 in 5shv

Go back to Magnesium Binding Sites List in 5shv
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-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-(6- Fluoropyridin-2-Yl)Piperidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.7
occ:1.00
 O B:HOH938 1.9 19.9 1.0
O B:HOH937 2.0 20.3 1.0
O B:HOH1029 2.0 23.5 1.0
O B:HOH934 2.1 17.7 1.0
O B:HOH1003 2.1 16.3 1.0
OD1 B:ASP564 2.1 21.4 1.0
CG B:ASP564 3.1 20.5 1.0
OD2 B:ASP564 3.4 22.8 1.0
O B:HOH1043 3.7 42.6 1.0
ZN B:ZN801 3.8 27.1 1.0
OE2 B:GLU592 4.0 25.0 1.0
O B:HOH1008 4.1 32.3 1.0
NE2 B:HIS595 4.1 22.1 1.0
OG1 B:THR633 4.2 20.0 1.0
CD2 B:HIS563 4.2 20.5 1.0
O B:HOH994 4.3 24.1 1.0
CD2 B:HIS595 4.3 22.6 1.0
CD2 B:HIS567 4.3 24.5 1.0
OD2 B:ASP674 4.4 23.9 1.0
O B:HIS563 4.4 23.3 1.0
CB B:ASP564 4.4 20.8 1.0
NE2 B:HIS567 4.5 23.2 1.0
O B:THR633 4.5 22.5 1.0
NE2 B:HIS563 4.6 21.5 1.0
CD2 B:HIS525 4.6 24.5 1.0
CB B:THR633 4.6 22.5 1.0
NE2 B:HIS525 4.7 25.1 1.0
CG B:GLU592 4.7 23.5 1.0
CA B:ASP564 4.8 21.2 1.0
CD B:GLU592 4.8 22.7 1.0

Magnesium binding site 3 out of 4 in 5shv

Go back to Magnesium Binding Sites List in 5shv
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-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-(6- Fluoropyridin-2-Yl)Piperidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.3
occ:1.00
 O C:HOH956 2.0 26.8 1.0
O C:HOH1008 2.0 24.0 1.0
O C:HOH937 2.0 19.8 1.0
OD1 C:ASP564 2.1 22.4 1.0
O C:HOH943 2.2 21.4 1.0
O C:HOH1024 2.2 22.6 1.0
CG C:ASP564 3.1 24.1 1.0
OD2 C:ASP564 3.5 24.5 1.0
O C:HOH1049 3.7 51.1 1.0
ZN C:ZN801 3.8 29.1 1.0
O C:HOH995 3.9 33.6 1.0
OE2 C:GLU592 4.0 29.1 1.0
NE2 C:HIS595 4.1 24.1 1.0
CD2 C:HIS563 4.2 25.0 1.0
OG1 C:THR633 4.2 24.5 1.0
CD2 C:HIS567 4.3 27.6 1.0
O C:HIS563 4.3 24.1 1.0
OD2 C:ASP674 4.3 30.2 1.0
O C:HOH1023 4.3 28.6 1.0
CD2 C:HIS595 4.4 23.0 1.0
O C:THR633 4.5 25.5 1.0
CB C:ASP564 4.5 23.2 1.0
NE2 C:HIS567 4.5 27.4 1.0
NE2 C:HIS563 4.6 25.7 1.0
CB C:THR633 4.7 25.1 1.0
CD2 C:HIS525 4.7 27.2 1.0
NE2 C:HIS525 4.7 27.4 1.0
CG C:GLU592 4.8 26.0 1.0
CD C:GLU592 4.8 27.0 1.0
CA C:ASP564 4.8 24.0 1.0

Magnesium binding site 4 out of 4 in 5shv

Go back to Magnesium Binding Sites List in 5shv
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(6- Fluoropyridin-2-Yl)Piperidin-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-(6- Fluoropyridin-2-Yl)Piperidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.3
occ:1.00
 O D:HOH980 2.0 24.9 1.0
O D:HOH986 2.1 30.1 1.0
O D:HOH930 2.1 22.4 1.0
O D:HOH915 2.1 25.7 1.0
OD1 D:ASP564 2.2 29.3 1.0
O D:HOH944 2.2 31.4 1.0
CG D:ASP564 3.2 29.4 1.0
OD2 D:ASP564 3.6 31.5 1.0
ZN D:ZN801 3.8 34.5 1.0
O D:HOH973 3.9 31.9 1.0
OE2 D:GLU592 3.9 34.7 1.0
O D:HOH979 4.1 33.9 1.0
NE2 D:HIS595 4.1 33.9 1.0
OG1 D:THR633 4.2 29.7 1.0
CD2 D:HIS567 4.3 35.0 1.0
CD2 D:HIS595 4.4 33.0 1.0
OD2 D:ASP674 4.4 35.5 1.0
CD2 D:HIS563 4.4 26.3 1.0
NE2 D:HIS567 4.4 33.2 1.0
O D:THR633 4.4 33.0 1.0
O D:HIS563 4.5 28.3 1.0
CB D:ASP564 4.5 30.6 1.0
CD2 D:HIS525 4.6 34.4 1.0
NE2 D:HIS525 4.7 35.0 1.0
CB D:THR633 4.7 30.0 1.0
CD D:GLU592 4.8 35.0 1.0
CG D:GLU592 4.8 35.6 1.0
NE2 D:HIS563 4.8 25.0 1.0
CA D:ASP564 4.9 28.8 1.0
O D:HOH985 5.0 36.6 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: Mon Sep 30 04:03:15 2024

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