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Magnesium in PDB 5skk: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5skk 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) 43.62 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.136, 135.136, 235.033, 90, 90, 120
R / Rfree (%) 19 / 24.2

Other elements in 5skk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide (pdb code 5skk). 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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide, PDB code: 5skk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skk

Go back to Magnesium Binding Sites List in 5skk
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.9
occ:1.00
 O A:HOH976 1.8 30.2 1.0
OD1 A:ASP564 1.9 34.8 1.0
O A:HOH957 2.0 27.9 1.0
O A:HOH949 2.0 27.9 1.0
O A:HOH927 2.1 30.1 1.0
O A:HOH920 2.2 31.8 1.0
CG A:ASP564 2.9 35.4 1.0
OD2 A:ASP564 3.3 35.4 1.0
ZN A:ZN801 3.7 37.3 1.0
O A:HOH973 3.9 40.6 1.0
OE2 A:GLU592 4.0 36.6 1.0
NE2 A:HIS595 4.0 33.0 1.0
CD2 A:HIS567 4.1 39.1 1.0
O A:HOH971 4.3 39.9 1.0
CB A:ASP564 4.3 35.3 1.0
CD2 A:HIS595 4.3 34.0 1.0
OG1 A:THR633 4.3 38.1 1.0
O A:HIS563 4.4 35.1 1.0
CD2 A:HIS563 4.4 31.1 1.0
NE2 A:HIS567 4.4 36.3 1.0
O A:THR633 4.6 37.6 1.0
OD2 A:ASP674 4.6 43.2 1.0
CD2 A:HIS525 4.7 37.3 1.0
NE2 A:HIS525 4.7 36.0 1.0
CA A:ASP564 4.7 34.2 1.0
NE2 A:HIS563 4.7 31.7 1.0
CB A:THR633 4.8 31.9 1.0
CD A:GLU592 4.8 39.0 1.0
CG A:GLU592 4.9 35.4 1.0

Magnesium binding site 2 out of 4 in 5skk

Go back to Magnesium Binding Sites List in 5skk
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.6
occ:1.00
 O B:HOH950 1.8 23.4 1.0
O B:HOH941 2.0 33.4 1.0
O B:HOH993 2.0 24.2 1.0
OD1 B:ASP564 2.0 30.6 1.0
O B:HOH948 2.1 26.3 1.0
O B:HOH922 2.1 25.1 1.0
CG B:ASP564 3.0 30.9 1.0
OD2 B:ASP564 3.4 34.7 1.0
ZN B:ZN801 3.7 35.5 1.0
O B:HOH933 3.9 47.6 1.0
OE2 B:GLU592 4.0 36.3 1.0
NE2 B:HIS595 4.1 36.5 1.0
CD2 B:HIS563 4.1 30.6 1.0
OG1 B:THR633 4.1 27.7 1.0
CD2 B:HIS595 4.3 37.3 1.0
O B:HIS563 4.3 36.0 1.0
CD2 B:HIS567 4.3 28.6 1.0
O B:HOH940 4.3 44.9 1.0
O B:HOH999 4.3 48.2 1.0
OD2 B:ASP674 4.3 34.7 1.0
CB B:ASP564 4.4 31.4 1.0
NE2 B:HIS563 4.5 28.7 1.0
O B:THR633 4.5 32.7 1.0
NE2 B:HIS567 4.5 29.6 1.0
CD2 B:HIS525 4.6 30.7 1.0
CB B:THR633 4.6 31.9 1.0
CA B:ASP564 4.7 33.0 1.0
NE2 B:HIS525 4.7 29.2 1.0
CG B:GLU592 4.8 39.1 1.0
CD B:GLU592 4.8 37.2 1.0

Magnesium binding site 3 out of 4 in 5skk

Go back to Magnesium Binding Sites List in 5skk
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.9
occ:1.00
 O C:HOH921 1.9 28.8 1.0
O C:HOH971 1.9 33.9 1.0
O C:HOH936 2.0 28.8 1.0
O C:HOH916 2.0 36.9 1.0
OD1 C:ASP564 2.1 31.3 1.0
O C:HOH920 2.2 32.2 1.0
CG C:ASP564 3.1 31.5 1.0
OD2 C:ASP564 3.5 32.3 1.0
ZN C:ZN801 3.7 40.7 1.0
O C:HOH946 3.8 47.8 1.0
CD2 C:HIS563 4.1 31.2 1.0
OE2 C:GLU592 4.1 35.5 1.0
OD2 C:ASP674 4.2 28.8 1.0
NE2 C:HIS595 4.3 33.8 1.0
OG1 C:THR633 4.3 37.4 1.0
O C:HIS563 4.3 33.6 1.0
CD2 C:HIS567 4.4 37.4 1.0
O C:HOH982 4.4 46.2 1.0
O C:THR633 4.4 38.4 1.0
CB C:ASP564 4.4 29.9 1.0
CD2 C:HIS595 4.5 34.1 1.0
NE2 C:HIS563 4.5 34.1 1.0
NE2 C:HIS567 4.6 36.7 1.0
CB C:THR633 4.6 35.1 1.0
O C:HOH962 4.7 43.9 1.0
CD2 C:HIS525 4.7 41.8 1.0
NE2 C:HIS525 4.8 45.0 1.0
CA C:ASP564 4.8 29.6 1.0
CG C:GLU592 4.8 35.8 1.0
CD C:GLU592 4.9 38.3 1.0

Magnesium binding site 4 out of 4 in 5skk

Go back to Magnesium Binding Sites List in 5skk
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-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 N-[1- Methyl-5-(Methylcarbamoyl)Pyrazol-4-Yl]-6-[(3S)-Oxolan-3-Yl]-3- (Pyrimidin-5-Ylamino)Pyrazine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:40.8
occ:1.00
 O D:HOH924 1.9 33.9 1.0
O D:HOH922 2.0 39.6 1.0
O D:HOH956 2.1 36.4 1.0
O D:HOH910 2.1 35.2 1.0
O D:HOH947 2.2 35.5 1.0
OD1 D:ASP564 2.2 42.0 1.0
CG D:ASP564 3.1 38.0 1.0
OD2 D:ASP564 3.4 46.8 1.0
ZN D:ZN801 3.6 46.7 1.0
OE2 D:GLU592 4.0 43.2 1.0
O D:HOH926 4.0 41.4 1.0
CD2 D:HIS563 4.2 35.9 1.0
O D:HOH952 4.2 45.5 1.0
OD2 D:ASP674 4.2 40.5 1.0
NE2 D:HIS595 4.3 43.9 1.0
OG1 D:THR633 4.3 40.4 1.0
CD2 D:HIS567 4.4 43.9 1.0
O D:HIS563 4.4 38.5 1.0
NE2 D:HIS563 4.4 34.0 1.0
CB D:ASP564 4.4 38.4 1.0
O D:THR633 4.5 46.5 1.0
CD2 D:HIS595 4.5 41.2 1.0
CB D:THR633 4.7 39.4 1.0
NE2 D:HIS567 4.7 47.9 1.0
CD2 D:HIS525 4.7 49.7 1.0
CA D:ASP564 4.8 34.3 1.0
OD1 D:ASP674 4.9 39.1 1.0
CD D:GLU592 4.9 45.3 1.0
NE2 D:HIS525 4.9 53.8 1.0
CG D:ASP674 5.0 38.8 1.0
CG D:GLU592 5.0 46.2 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: Tue Aug 12 20:18:19 2025

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