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Magnesium in PDB 5sju: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sju 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) 43.63 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.633, 135.633, 235.654, 90, 90, 120
R / Rfree (%) 17.6 / 22

Other elements in 5sju:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide 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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5sju). 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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5sju:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sju

Go back to Magnesium Binding Sites List in 5sju
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.8
occ:1.00
 O A:HOH997 1.9 26.0 1.0
O A:HOH934 2.0 23.6 1.0
O A:HOH1028 2.0 26.5 1.0
OD1 A:ASP564 2.0 25.6 1.0
O A:HOH946 2.2 23.5 1.0
O A:HOH984 2.2 23.9 1.0
CG A:ASP564 3.0 26.9 1.0
OD2 A:ASP564 3.3 26.0 1.0
ZN A:ZN801 3.7 31.8 1.0
O A:HOH976 3.9 38.2 1.0
O A:HOH1018 4.0 45.9 1.0
NE2 A:HIS595 4.1 25.6 1.0
OE2 A:GLU592 4.2 31.2 1.0
OG1 A:THR633 4.2 27.8 1.0
CD2 A:HIS567 4.3 29.1 1.0
O A:HOH989 4.3 36.0 1.0
CD2 A:HIS563 4.3 24.2 1.0
O A:HIS563 4.3 27.9 1.0
CB A:ASP564 4.4 26.8 1.0
CD2 A:HIS595 4.4 23.6 1.0
NE2 A:HIS567 4.5 28.0 1.0
O A:THR633 4.5 29.0 1.0
OD2 A:ASP674 4.5 33.5 1.0
CD2 A:HIS525 4.6 30.9 1.0
NE2 A:HIS525 4.6 29.4 1.0
NE2 A:HIS563 4.6 25.1 1.0
CB A:THR633 4.7 24.6 1.0
CA A:ASP564 4.8 28.9 1.0
CG A:GLU592 4.9 27.1 1.0
CD A:GLU592 4.9 31.1 1.0

Magnesium binding site 2 out of 4 in 5sju

Go back to Magnesium Binding Sites List in 5sju
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.2
occ:1.00
 O B:HOH960 2.0 23.9 1.0
O B:HOH985 2.0 21.8 1.0
O B:HOH957 2.1 24.1 1.0
O B:HOH997 2.1 23.3 1.0
O B:HOH1020 2.1 24.6 1.0
OD1 B:ASP564 2.1 24.3 1.0
CG B:ASP564 3.1 22.9 1.0
OD2 B:ASP564 3.4 23.7 1.0
ZN B:ZN801 3.7 30.4 1.0
O B:HOH989 4.0 44.0 1.0
OE2 B:GLU592 4.1 30.8 1.0
NE2 B:HIS595 4.1 27.4 1.0
O B:HOH991 4.2 39.9 1.0
OG1 B:THR633 4.2 22.1 1.0
CD2 B:HIS563 4.2 22.1 1.0
O B:HIS563 4.3 26.4 1.0
CD2 B:HIS567 4.3 27.7 1.0
CD2 B:HIS595 4.4 27.3 1.0
O B:HOH983 4.4 35.0 1.0
OD2 B:ASP674 4.5 27.9 1.0
CB B:ASP564 4.5 21.4 1.0
O B:THR633 4.5 24.7 1.0
NE2 B:HIS567 4.5 24.2 1.0
NE2 B:HIS563 4.6 21.3 1.0
CD2 B:HIS525 4.6 30.0 1.0
CB B:THR633 4.7 25.2 1.0
NE2 B:HIS525 4.7 29.1 1.0
CA B:ASP564 4.8 23.1 1.0
CG B:GLU592 4.8 26.5 1.0
CD B:GLU592 4.8 28.4 1.0

Magnesium binding site 3 out of 4 in 5sju

Go back to Magnesium Binding Sites List in 5sju
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.5
occ:1.00
 O C:HOH967 2.0 22.8 1.0
O C:HOH1047 2.0 25.1 1.0
O C:HOH964 2.0 29.0 1.0
O C:HOH992 2.0 24.1 1.0
OD1 C:ASP564 2.1 25.9 1.0
O C:HOH951 2.2 24.6 1.0
CG C:ASP564 3.1 28.6 1.0
OD2 C:ASP564 3.4 25.8 1.0
ZN C:ZN801 3.7 31.9 1.0
O C:HOH932 3.8 48.4 1.0
NE2 C:HIS595 4.0 27.4 1.0
O C:HOH1037 4.1 43.3 1.0
OE2 C:GLU592 4.1 32.3 1.0
OG1 C:THR633 4.2 27.9 1.0
CD2 C:HIS563 4.2 26.3 1.0
CD2 C:HIS567 4.2 32.4 1.0
O C:HOH1012 4.2 33.6 1.0
O C:HIS563 4.3 26.5 1.0
CD2 C:HIS595 4.4 26.8 1.0
OD2 C:ASP674 4.4 34.5 1.0
CB C:ASP564 4.4 25.2 1.0
NE2 C:HIS567 4.4 31.4 1.0
O C:THR633 4.6 28.3 1.0
NE2 C:HIS563 4.6 28.6 1.0
CD2 C:HIS525 4.6 29.4 1.0
CB C:THR633 4.7 25.4 1.0
NE2 C:HIS525 4.7 33.0 1.0
CA C:ASP564 4.8 26.3 1.0
CG C:GLU592 4.9 26.4 1.0
CD C:GLU592 4.9 28.4 1.0

Magnesium binding site 4 out of 4 in 5sju

Go back to Magnesium Binding Sites List in 5sju
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide


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-N-[4-(Piperidin-1-Ylmethyl)-1,3-Thiazol-2-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.3
occ:1.00
 O D:HOH952 2.0 28.1 1.0
O D:HOH931 2.1 32.1 1.0
O D:HOH983 2.1 26.7 1.0
OD1 D:ASP564 2.1 31.3 1.0
O D:HOH928 2.1 30.2 1.0
O D:HOH967 2.2 29.9 1.0
CG D:ASP564 3.1 28.3 1.0
OD2 D:ASP564 3.5 34.0 1.0
ZN D:ZN801 3.7 35.2 1.0
O D:HOH939 3.8 44.4 1.0
OE2 D:GLU592 4.1 34.4 1.0
NE2 D:HIS595 4.1 32.6 1.0
OG1 D:THR633 4.2 29.8 1.0
CD2 D:HIS563 4.2 28.9 1.0
O D:HOH978 4.3 43.9 1.0
CD2 D:HIS567 4.3 33.9 1.0
CD2 D:HIS595 4.3 31.8 1.0
O D:HIS563 4.4 29.2 1.0
OD2 D:ASP674 4.4 33.0 1.0
CB D:ASP564 4.5 28.5 1.0
NE2 D:HIS567 4.5 30.6 1.0
O D:THR633 4.5 32.5 1.0
CD2 D:HIS525 4.6 35.6 1.0
NE2 D:HIS563 4.6 25.3 1.0
NE2 D:HIS525 4.6 43.7 1.0
CB D:THR633 4.7 28.6 1.0
CA D:ASP564 4.8 29.3 1.0
CG D:GLU592 4.9 34.9 1.0
CD D:GLU592 4.9 38.1 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 04:27:07 2024

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