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Magnesium in PDB 5sjb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline, PDB code: 5sjb was solved by C.Joseph, J.Benz, A.Flohr, A.Krasso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.60 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.538, 135.538, 235.689, 90, 90, 120
R / Rfree (%) 18.7 / 23.3

Other elements in 5sjb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline (pdb code 5sjb). 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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline, PDB code: 5sjb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjb

Go back to Magnesium Binding Sites List in 5sjb
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:17.6
occ:1.00
 O A:HOH1022 1.9 16.8 1.0
OD1 A:ASP564 2.0 18.0 1.0
O A:HOH913 2.1 20.9 1.0
O A:HOH961 2.1 14.6 1.0
O A:HOH967 2.1 22.6 1.0
O A:HOH954 2.2 12.6 1.0
CG A:ASP564 2.9 18.6 1.0
OD2 A:ASP564 3.3 19.8 1.0
ZN A:ZN801 3.7 23.3 1.0
O A:HOH1015 3.8 30.9 1.0
O A:HOH1046 3.9 45.8 1.0
NE2 A:HIS595 4.1 19.9 1.0
OE2 A:GLU592 4.1 27.6 1.0
CD2 A:HIS567 4.2 23.6 1.0
CD2 A:HIS563 4.3 17.7 1.0
OG1 A:THR633 4.3 22.4 1.0
CB A:ASP564 4.3 19.0 1.0
CD2 A:HIS595 4.3 19.8 1.0
O A:HIS563 4.4 20.2 1.0
OD2 A:ASP674 4.4 30.1 1.0
O A:HOH1018 4.5 30.4 1.0
NE2 A:HIS567 4.5 23.8 1.0
NE2 A:HIS563 4.5 18.1 1.0
CD2 A:HIS525 4.5 24.1 1.0
NE2 A:HIS525 4.6 24.2 1.0
O A:THR633 4.6 25.3 1.0
CA A:ASP564 4.7 19.4 1.0
CB A:THR633 4.8 21.6 1.0
CD A:GLU592 4.9 26.2 1.0
CG A:GLU592 4.9 24.0 1.0

Magnesium binding site 2 out of 4 in 5sjb

Go back to Magnesium Binding Sites List in 5sjb
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:13.7
occ:1.00
 O B:HOH940 2.0 17.4 1.0
O B:HOH952 2.0 14.0 1.0
O B:HOH925 2.0 16.2 1.0
OD1 B:ASP564 2.0 16.5 1.0
O B:HOH929 2.0 15.5 1.0
O B:HOH982 2.0 15.4 1.0
CG B:ASP564 3.1 17.6 1.0
OD2 B:ASP564 3.4 17.6 1.0
ZN B:ZN801 3.8 24.8 1.0
O B:HOH1004 3.9 32.0 1.0
NE2 B:HIS595 4.0 23.4 1.0
OE2 B:GLU592 4.0 22.5 1.0
CD2 B:HIS563 4.2 16.5 1.0
CD2 B:HIS567 4.2 19.8 1.0
OG1 B:THR633 4.3 21.2 1.0
O B:HOH1001 4.3 25.4 1.0
CD2 B:HIS595 4.3 24.2 1.0
OD2 B:ASP674 4.3 23.4 1.0
NE2 B:HIS567 4.4 19.9 1.0
CB B:ASP564 4.4 17.1 1.0
O B:HIS563 4.5 18.7 1.0
CD2 B:HIS525 4.5 22.4 1.0
NE2 B:HIS563 4.5 16.2 1.0
O B:THR633 4.6 20.1 1.0
NE2 B:HIS525 4.6 22.1 1.0
CB B:THR633 4.7 20.8 1.0
CG B:GLU592 4.7 22.6 1.0
CA B:ASP564 4.8 18.3 1.0
CD B:GLU592 4.8 23.1 1.0

Magnesium binding site 3 out of 4 in 5sjb

Go back to Magnesium Binding Sites List in 5sjb
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:20.6
occ:1.00
 O C:HOH975 2.0 18.8 1.0
O C:HOH940 2.0 15.3 1.0
O C:HOH1032 2.0 20.5 1.0
O C:HOH959 2.1 18.3 1.0
O C:HOH981 2.1 19.6 1.0
OD1 C:ASP564 2.1 19.4 1.0
CG C:ASP564 3.1 20.1 1.0
OD2 C:ASP564 3.5 21.2 1.0
O C:HOH1050 3.8 51.2 1.0
O C:HOH1027 3.8 31.5 1.0
ZN C:ZN801 3.9 26.6 1.0
NE2 C:HIS595 4.1 21.9 1.0
OE2 C:GLU592 4.1 26.4 1.0
CD2 C:HIS567 4.2 26.0 1.0
O C:HOH995 4.3 28.4 1.0
CD2 C:HIS563 4.3 17.4 1.0
OG1 C:THR633 4.3 22.0 1.0
O C:HIS563 4.4 18.9 1.0
NE2 C:HIS567 4.4 26.1 1.0
OD2 C:ASP674 4.4 25.7 1.0
CD2 C:HIS595 4.4 21.6 1.0
CB C:ASP564 4.5 19.2 1.0
O C:THR633 4.5 24.2 1.0
CD2 C:HIS525 4.6 25.8 1.0
NE2 C:HIS563 4.6 18.8 1.0
NE2 C:HIS525 4.8 24.9 1.0
CB C:THR633 4.8 21.6 1.0
CA C:ASP564 4.8 19.6 1.0
CG C:GLU592 4.8 25.6 1.0
CD C:GLU592 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 5sjb

Go back to Magnesium Binding Sites List in 5sjb
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]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- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:28.3
occ:1.00
 O D:HOH989 2.0 30.3 1.0
O D:HOH947 2.1 22.9 1.0
OD1 D:ASP564 2.1 26.6 1.0
O D:HOH937 2.1 25.4 1.0
O D:HOH975 2.1 28.5 1.0
O D:HOH944 2.2 29.0 1.0
CG D:ASP564 3.1 27.7 1.0
OD2 D:ASP564 3.5 34.5 1.0
O D:HOH967 3.8 38.4 1.0
ZN D:ZN801 3.8 33.8 1.0
O D:HOH959 3.9 28.0 1.0
NE2 D:HIS595 4.0 33.2 1.0
OE2 D:GLU592 4.1 31.9 1.0
CD2 D:HIS567 4.2 39.7 1.0
OG1 D:THR633 4.3 32.0 1.0
CD2 D:HIS595 4.3 32.7 1.0
CD2 D:HIS563 4.4 24.2 1.0
O D:HIS563 4.4 26.6 1.0
NE2 D:HIS567 4.5 40.4 1.0
CB D:ASP564 4.5 27.6 1.0
OD2 D:ASP674 4.5 33.3 1.0
O D:THR633 4.6 38.4 1.0
NE2 D:HIS563 4.7 24.2 1.0
CD2 D:HIS525 4.8 33.0 1.0
CB D:THR633 4.8 34.1 1.0
NE2 D:HIS525 4.8 32.7 1.0
CA D:ASP564 4.8 27.3 1.0
CD D:GLU592 4.9 34.0 1.0
CG D:GLU592 4.9 34.6 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: Tue Aug 12 20:05:32 2025

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