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Magnesium in PDB 5sgq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid, PDB code: 5sgq was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.59 / 2.04
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.496, 135.496, 235.736, 90, 90, 120
R / Rfree (%) 17.7 / 22.4

Other elements in 5sgq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid 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 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid (pdb code 5sgq). 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- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid, PDB code: 5sgq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgq

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.1
occ:1.00
 OD1 A:ASP564 2.0 24.7 1.0
O A:HOH960 2.0 21.6 1.0
O A:HOH921 2.0 27.2 1.0
O A:HOH1014 2.0 24.5 1.0
O A:HOH961 2.2 22.7 1.0
O A:HOH924 2.2 27.1 1.0
CG A:ASP564 3.0 27.5 1.0
OD2 A:ASP564 3.3 27.9 1.0
ZN A:ZN801 3.8 30.0 1.0
O A:HOH995 4.0 36.2 1.0
NE2 A:HIS595 4.0 31.8 1.0
OE2 A:GLU592 4.0 30.4 1.0
CD2 A:HIS567 4.2 29.7 1.0
O A:HOH985 4.2 39.6 1.0
CD2 A:HIS595 4.3 27.7 1.0
OG1 A:THR633 4.3 28.9 1.0
CD2 A:HIS563 4.3 20.5 1.0
CB A:ASP564 4.4 23.0 1.0
NE2 A:HIS567 4.4 28.8 1.0
O A:HIS563 4.4 28.8 1.0
OD2 A:ASP674 4.5 32.5 1.0
O A:THR633 4.5 29.1 1.0
CD2 A:HIS525 4.6 29.4 1.0
NE2 A:HIS563 4.6 23.9 1.0
NE2 A:HIS525 4.6 30.2 1.0
CA A:ASP564 4.8 26.8 1.0
CB A:THR633 4.8 27.8 1.0
CG A:GLU592 4.9 24.9 1.0
CD A:GLU592 4.9 27.4 1.0

Magnesium binding site 2 out of 4 in 5sgq

Go back to Magnesium Binding Sites List in 5sgq
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.9
occ:1.00
 O B:HOH944 1.9 22.0 1.0
O B:HOH942 2.0 20.1 1.0
O B:HOH916 2.0 20.4 1.0
OD1 B:ASP564 2.0 25.2 1.0
O B:HOH992 2.1 26.2 1.0
O B:HOH975 2.1 21.1 1.0
CG B:ASP564 3.1 23.8 1.0
OD2 B:ASP564 3.5 26.9 1.0
ZN B:ZN801 3.8 29.4 1.0
OE2 B:GLU592 3.9 29.9 1.0
O B:HOH968 4.0 33.5 1.0
NE2 B:HIS595 4.1 26.5 1.0
OG1 B:THR633 4.2 22.9 1.0
CD2 B:HIS563 4.2 23.8 1.0
CD2 B:HIS567 4.3 29.4 1.0
OD2 B:ASP674 4.3 27.6 1.0
O B:HIS563 4.4 28.2 1.0
O B:HOH966 4.4 36.8 1.0
CD2 B:HIS595 4.4 27.2 1.0
CB B:ASP564 4.4 25.3 1.0
NE2 B:HIS567 4.5 26.0 1.0
O B:THR633 4.5 25.4 1.0
CB B:THR633 4.6 23.5 1.0
CD2 B:HIS525 4.6 30.3 1.0
NE2 B:HIS525 4.7 26.9 1.0
NE2 B:HIS563 4.7 19.7 1.0
CA B:ASP564 4.8 24.1 1.0
CD B:GLU592 4.8 28.5 1.0
CG B:GLU592 4.8 29.3 1.0

Magnesium binding site 3 out of 4 in 5sgq

Go back to Magnesium Binding Sites List in 5sgq
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.5
occ:1.00
 O C:HOH985 2.0 24.6 1.0
O C:HOH939 2.0 25.4 1.0
O C:HOH1022 2.1 25.8 1.0
O C:HOH957 2.1 26.2 1.0
OD1 C:ASP564 2.1 28.8 1.0
O C:HOH951 2.1 25.3 1.0
CG C:ASP564 3.1 27.9 1.0
OD2 C:ASP564 3.4 26.5 1.0
ZN C:ZN801 3.8 31.7 1.0
O C:HOH1000 4.0 30.8 1.0
NE2 C:HIS595 4.0 29.2 1.0
OE2 C:GLU592 4.1 32.3 1.0
CD2 C:HIS567 4.2 30.0 1.0
CD2 C:HIS563 4.3 23.8 1.0
OG1 C:THR633 4.3 28.9 1.0
O C:HIS563 4.3 24.4 1.0
CD2 C:HIS595 4.3 27.1 1.0
NE2 C:HIS567 4.4 28.9 1.0
O C:HOH995 4.4 39.9 1.0
OD2 C:ASP674 4.4 33.1 1.0
CB C:ASP564 4.5 24.9 1.0
O C:THR633 4.6 29.8 1.0
CB C:THR633 4.7 28.4 1.0
NE2 C:HIS563 4.7 26.1 1.0
CD2 C:HIS525 4.7 34.5 1.0
NE2 C:HIS525 4.7 35.7 1.0
CA C:ASP564 4.8 27.9 1.0
CG C:GLU592 4.8 26.2 1.0
CD C:GLU592 4.9 32.6 1.0

Magnesium binding site 4 out of 4 in 5sgq

Go back to Magnesium Binding Sites List in 5sgq
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid


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- Cyclopropyl-3-(Pyrimidin-5-Ylamino)Pyrazine-2-Carboxylic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.6
occ:1.00
 O D:HOH978 2.0 33.3 1.0
O D:HOH932 2.0 36.0 1.0
O D:HOH914 2.1 24.3 1.0
OD1 D:ASP564 2.1 30.3 1.0
O D:HOH934 2.1 28.5 1.0
O D:HOH972 2.1 24.3 1.0
CG D:ASP564 3.1 26.2 1.0
OD2 D:ASP564 3.4 38.6 1.0
ZN D:ZN801 3.8 36.2 1.0
O D:HOH964 4.0 30.5 1.0
O D:HOH955 4.0 44.1 1.0
NE2 D:HIS595 4.1 34.2 1.0
OE2 D:GLU592 4.1 36.3 1.0
OG1 D:THR633 4.2 32.4 1.0
CD2 D:HIS563 4.2 34.0 1.0
CD2 D:HIS567 4.3 42.5 1.0
O D:HIS563 4.3 33.6 1.0
CD2 D:HIS595 4.3 33.7 1.0
OD2 D:ASP674 4.4 34.6 1.0
CB D:ASP564 4.4 30.0 1.0
NE2 D:HIS567 4.5 37.8 1.0
O D:THR633 4.5 33.9 1.0
NE2 D:HIS563 4.6 29.5 1.0
CD2 D:HIS525 4.6 40.1 1.0
CB D:THR633 4.7 29.8 1.0
NE2 D:HIS525 4.7 39.0 1.0
CA D:ASP564 4.8 28.9 1.0
CG D:GLU592 4.9 40.5 1.0
CD D:GLU592 4.9 36.7 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 03:49:28 2024

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