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Magnesium in PDB 5sjx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline, PDB code: 5sjx 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) 43.77 / 2.06
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.65, 135.65, 235.91, 90, 90, 120
R / Rfree (%) 18 / 23.7

Other elements in 5sjx:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline 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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline (pdb code 5sjx). 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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline, PDB code: 5sjx:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjx

Go back to Magnesium Binding Sites List in 5sjx
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.9
occ:1.00
 OD1 A:ASP564 2.0 21.9 1.0
O A:HOH944 2.0 24.9 1.0
O A:HOH1008 2.1 27.7 1.0
O A:HOH916 2.1 19.4 1.0
O A:HOH989 2.1 29.6 1.0
O A:HOH925 2.1 24.5 1.0
CG A:ASP564 3.1 24.7 1.0
OD2 A:ASP564 3.4 26.7 1.0
O A:HOH1017 3.5 33.7 1.0
O A:HOH929 3.7 32.2 1.0
ZN A:ZN801 3.7 30.1 1.0
NE2 A:HIS595 4.0 23.8 1.0
O A:HOH939 4.1 40.6 1.0
OE2 A:GLU592 4.1 23.8 1.0
O A:HOH1005 4.2 29.6 1.0
CD2 A:HIS567 4.3 23.2 1.0
OG1 A:THR633 4.4 26.7 1.0
O A:THR633 4.4 25.9 1.0
O A:HIS563 4.4 24.6 1.0
CD2 A:HIS595 4.4 20.2 1.0
CB A:ASP564 4.4 21.9 1.0
CD2 A:HIS563 4.5 22.8 1.0
CD2 A:HIS525 4.6 28.4 1.0
NE2 A:HIS567 4.6 22.6 1.0
NE2 A:HIS525 4.7 23.6 1.0
OD2 A:ASP674 4.7 30.6 1.0
NE2 A:HIS563 4.7 23.1 1.0
CB A:THR633 4.7 28.3 1.0
O A:HOH1015 4.8 30.1 1.0
CA A:ASP564 4.9 24.9 1.0
CD A:GLU592 4.9 26.0 1.0
CG A:GLU592 4.9 24.5 1.0

Magnesium binding site 2 out of 4 in 5sjx

Go back to Magnesium Binding Sites List in 5sjx
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:15.3
occ:1.00
 O B:HOH951 2.0 14.9 1.0
O B:HOH947 2.0 16.3 1.0
O B:HOH916 2.0 17.1 1.0
O B:HOH961 2.0 17.1 1.0
O B:HOH1023 2.1 16.7 1.0
OD1 B:ASP564 2.1 23.2 1.0
CG B:ASP564 3.1 19.2 1.0
O B:HOH1030 3.4 30.2 1.0
OD2 B:ASP564 3.4 22.0 1.0
ZN B:ZN801 3.7 26.3 1.0
O B:HOH1027 3.8 33.9 1.0
OE2 B:GLU592 4.0 22.3 1.0
NE2 B:HIS595 4.0 19.0 1.0
O B:HOH984 4.1 25.7 1.0
OG1 B:THR633 4.2 22.4 1.0
CD2 B:HIS563 4.2 20.4 1.0
CD2 B:HIS595 4.3 21.7 1.0
O B:HIS563 4.3 23.5 1.0
CD2 B:HIS567 4.3 26.6 1.0
NE2 B:HIS563 4.5 20.6 1.0
CB B:ASP564 4.5 18.2 1.0
O B:HOH907 4.5 49.9 1.0
NE2 B:HIS567 4.5 25.2 1.0
O B:THR633 4.5 19.6 1.0
OD2 B:ASP674 4.5 21.7 1.0
CD2 B:HIS525 4.6 21.7 1.0
CB B:THR633 4.7 21.3 1.0
CA B:ASP564 4.8 20.0 1.0
NE2 B:HIS525 4.8 24.8 1.0
CG B:GLU592 4.9 24.3 1.0
CD B:GLU592 4.9 24.8 1.0

Magnesium binding site 3 out of 4 in 5sjx

Go back to Magnesium Binding Sites List in 5sjx
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.4
occ:1.00
 OD1 C:ASP564 2.0 22.5 1.0
O C:HOH1001 2.0 21.7 1.0
O C:HOH955 2.1 23.9 1.0
O C:HOH959 2.1 19.5 1.0
O C:HOH948 2.1 21.9 1.0
O C:HOH1012 2.2 23.7 1.0
CG C:ASP564 3.0 22.4 1.0
OD2 C:ASP564 3.4 21.1 1.0
O C:HOH976 3.6 34.3 1.0
O C:HOH1002 3.7 32.7 1.0
ZN C:ZN801 3.8 28.2 1.0
NE2 C:HIS595 3.9 25.1 1.0
OE2 C:GLU592 4.0 28.7 1.0
O C:HOH930 4.1 39.1 1.0
O C:HOH953 4.1 30.9 1.0
CD2 C:HIS567 4.2 24.0 1.0
CD2 C:HIS595 4.2 25.4 1.0
O C:HIS563 4.2 23.7 1.0
OG1 C:THR633 4.2 22.4 1.0
CD2 C:HIS563 4.3 20.2 1.0
CB C:ASP564 4.4 20.8 1.0
O C:THR633 4.4 22.4 1.0
OD2 C:ASP674 4.5 27.9 1.0
NE2 C:HIS567 4.5 22.4 1.0
CD2 C:HIS525 4.6 25.8 1.0
CB C:THR633 4.7 22.1 1.0
NE2 C:HIS525 4.8 27.8 1.0
CA C:ASP564 4.8 23.2 1.0
NE2 C:HIS563 4.8 24.6 1.0
CG C:GLU592 4.8 24.4 1.0
CD C:GLU592 4.9 26.4 1.0
CE1 C:HIS595 5.0 24.2 1.0

Magnesium binding site 4 out of 4 in 5sjx

Go back to Magnesium Binding Sites List in 5sjx
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.7
occ:1.00
 O D:HOH934 2.0 29.5 1.0
O D:HOH936 2.1 36.2 1.0
OD1 D:ASP564 2.1 34.8 1.0
O D:HOH947 2.1 28.4 1.0
O D:HOH951 2.1 30.7 1.0
O D:HOH917 2.3 27.9 1.0
CG D:ASP564 3.1 34.0 1.0
O D:HOH958 3.2 38.2 1.0
OD2 D:ASP564 3.3 40.2 1.0
ZN D:ZN801 3.7 41.6 1.0
O D:HOH970 4.0 35.5 1.0
OE2 D:GLU592 4.1 37.4 1.0
NE2 D:HIS595 4.2 34.2 1.0
CD2 D:HIS567 4.3 34.6 1.0
OG1 D:THR633 4.3 37.2 1.0
CD2 D:HIS563 4.4 25.1 1.0
CD2 D:HIS525 4.4 37.4 1.0
NE2 D:HIS525 4.4 38.9 1.0
CB D:ASP564 4.5 32.4 1.0
OD2 D:ASP674 4.5 35.4 1.0
O D:HIS563 4.5 29.9 1.0
CD2 D:HIS595 4.5 33.0 1.0
NE2 D:HIS567 4.6 35.6 1.0
O D:THR633 4.6 46.5 1.0
NE2 D:HIS563 4.7 25.9 1.0
CB D:THR633 4.8 35.8 1.0
O D:HOH976 4.8 36.6 1.0
CA D:ASP564 4.8 30.3 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 04:27:33 2024

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