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Magnesium in PDB 5skm: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine, PDB code: 5skm was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 1.91
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.021, 136.021, 236.102, 90, 90, 120
R / Rfree (%) 18 / 22.1

Other elements in 5skm:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine (pdb code 5skm). 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 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine, PDB code: 5skm:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skm

Go back to Magnesium Binding Sites List in 5skm
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-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 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.7
occ:1.00
 O A:HOH1027 1.9 27.8 1.0
O A:HOH919 2.0 22.8 1.0
OD1 A:ASP564 2.0 24.4 1.0
O A:HOH989 2.0 25.9 1.0
O A:HOH970 2.1 22.1 1.0
O A:HOH929 2.2 22.5 1.0
CG A:ASP564 3.0 28.0 1.0
OD2 A:ASP564 3.4 25.6 1.0
ZN A:ZN801 3.7 30.8 1.0
O A:HOH952 3.9 34.0 1.0
O A:HOH957 4.0 46.8 1.0
OE2 A:GLU592 4.0 27.9 1.0
NE2 A:HIS595 4.1 25.8 1.0
O A:HOH984 4.2 31.9 1.0
CD2 A:HIS567 4.2 28.5 1.0
O A:HOH901 4.3 46.3 1.0
O A:HIS563 4.3 26.4 1.0
OG1 A:THR633 4.3 26.5 1.0
CD2 A:HIS563 4.4 25.1 1.0
CD2 A:HIS595 4.4 21.1 1.0
NE2 A:HIS567 4.4 26.4 1.0
CB A:ASP564 4.4 24.8 1.0
CD2 A:HIS525 4.6 28.8 1.0
OD2 A:ASP674 4.6 32.3 1.0
O A:THR633 4.6 29.1 1.0
NE2 A:HIS525 4.6 31.0 1.0
NE2 A:HIS563 4.7 26.8 1.0
CB A:THR633 4.7 26.1 1.0
CG A:GLU592 4.8 29.9 1.0
CD A:GLU592 4.8 30.2 1.0
CA A:ASP564 4.8 25.0 1.0

Magnesium binding site 2 out of 4 in 5skm

Go back to Magnesium Binding Sites List in 5skm
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-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 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.8
occ:1.00
 O B:HOH965 2.0 22.2 1.0
O B:HOH953 2.0 22.2 1.0
O B:HOH1036 2.1 23.2 1.0
OD1 B:ASP564 2.1 23.9 1.0
O B:HOH1016 2.1 20.8 1.0
O B:HOH949 2.1 24.1 1.0
CG B:ASP564 3.1 23.8 1.0
OD2 B:ASP564 3.4 22.0 1.0
O B:HOH901 3.7 40.5 1.0
ZN B:ZN801 3.7 28.6 1.0
O B:HOH1040 4.0 33.3 1.0
OE2 B:GLU592 4.1 30.4 1.0
NE2 B:HIS595 4.1 23.8 1.0
O B:HOH1004 4.1 30.5 1.0
OG1 B:THR633 4.2 23.5 1.0
CD2 B:HIS563 4.2 22.8 1.0
O B:HIS563 4.3 26.6 1.0
CD2 B:HIS567 4.3 27.7 1.0
O B:HOH982 4.3 28.2 1.0
CD2 B:HIS595 4.4 24.0 1.0
CB B:ASP564 4.4 21.8 1.0
NE2 B:HIS563 4.5 22.5 1.0
OD2 B:ASP674 4.5 26.0 1.0
NE2 B:HIS567 4.5 23.8 1.0
O B:THR633 4.6 24.2 1.0
CD2 B:HIS525 4.6 28.2 1.0
CB B:THR633 4.7 24.6 1.0
NE2 B:HIS525 4.7 30.7 1.0
CG B:GLU592 4.8 27.1 1.0
CA B:ASP564 4.8 23.8 1.0
CD B:GLU592 4.9 24.6 1.0

Magnesium binding site 3 out of 4 in 5skm

Go back to Magnesium Binding Sites List in 5skm
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-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 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.6
occ:1.00
 OD1 C:ASP564 2.0 23.7 1.0
O C:HOH988 2.0 25.6 1.0
O C:HOH931 2.0 22.0 1.0
O C:HOH1040 2.1 23.7 1.0
O C:HOH956 2.1 24.4 1.0
O C:HOH942 2.2 21.1 1.0
CG C:ASP564 3.0 26.6 1.0
OD2 C:ASP564 3.4 22.5 1.0
ZN C:ZN801 3.7 29.7 1.0
O C:HOH902 3.7 40.1 1.0
O C:HOH1016 4.0 36.9 1.0
NE2 C:HIS595 4.0 27.7 1.0
O C:HOH1013 4.1 30.7 1.0
OE2 C:GLU592 4.1 30.7 1.0
CD2 C:HIS563 4.2 22.9 1.0
OG1 C:THR633 4.2 24.4 1.0
O C:HIS563 4.3 24.8 1.0
CD2 C:HIS595 4.3 25.2 1.0
O C:HOH1004 4.3 26.7 1.0
CD2 C:HIS567 4.3 28.6 1.0
OD2 C:ASP674 4.4 34.2 1.0
CB C:ASP564 4.4 25.0 1.0
NE2 C:HIS567 4.5 26.2 1.0
NE2 C:HIS563 4.5 26.3 1.0
O C:THR633 4.5 24.8 1.0
CD2 C:HIS525 4.6 29.6 1.0
CB C:THR633 4.7 26.1 1.0
NE2 C:HIS525 4.7 28.2 1.0
CA C:ASP564 4.8 26.4 1.0
CG C:GLU592 4.8 24.7 1.0
CD C:GLU592 4.9 25.9 1.0

Magnesium binding site 4 out of 4 in 5skm

Go back to Magnesium Binding Sites List in 5skm
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-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 6- Chloro-N,N-Dimethyl-2-[2-(1-Pyridin-2-Ylpyrrolidin-3-Yl) Ethyl]Quinazolin-4-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.7
occ:1.00
 O D:HOH960 2.1 29.6 1.0
O D:HOH952 2.1 29.7 1.0
O D:HOH938 2.1 30.9 1.0
O D:HOH932 2.1 29.7 1.0
O D:HOH965 2.1 31.3 1.0
OD1 D:ASP564 2.1 36.4 1.0
CG D:ASP564 3.1 34.2 1.0
OD2 D:ASP564 3.4 33.5 1.0
ZN D:ZN801 3.7 36.7 1.0
O D:HOH974 3.8 40.1 1.0
OE2 D:GLU592 4.1 36.9 1.0
NE2 D:HIS595 4.1 33.0 1.0
OG1 D:THR633 4.2 36.4 1.0
O D:HOH987 4.2 37.2 1.0
CD2 D:HIS563 4.3 34.1 1.0
CD2 D:HIS567 4.3 35.8 1.0
CD2 D:HIS595 4.3 30.6 1.0
O D:HIS563 4.4 31.4 1.0
OD2 D:ASP674 4.5 39.1 1.0
CB D:ASP564 4.5 30.3 1.0
O D:THR633 4.5 37.1 1.0
CD2 D:HIS525 4.5 38.5 1.0
NE2 D:HIS525 4.6 43.4 1.0
NE2 D:HIS567 4.6 34.3 1.0
CB D:THR633 4.7 36.9 1.0
NE2 D:HIS563 4.7 27.4 1.0
CG D:GLU592 4.9 37.9 1.0
CA D:ASP564 4.9 30.6 1.0
CD D:GLU592 4.9 37.2 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: Mon Sep 30 04:37:22 2024

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