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Magnesium in PDB 5skv: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5skv 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) 43.51 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.283, 135.283, 234.745, 90, 90, 120
R / Rfree (%) 19.9 / 25.5

Other elements in 5skv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5skv). 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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5skv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skv

Go back to Magnesium Binding Sites List in 5skv
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:40.7
occ:1.00
 O A:HOH938 1.9 29.7 1.0
O A:HOH947 1.9 36.1 1.0
O A:HOH941 2.1 28.9 1.0
OD1 A:ASP564 2.1 34.4 1.0
O A:HOH973 2.3 40.8 1.0
CG A:ASP564 3.2 38.1 1.0
OD2 A:ASP564 3.6 36.8 1.0
OE2 A:GLU592 3.8 40.0 1.0
NE2 A:HIS595 3.8 41.0 1.0
O A:HOH966 3.8 35.5 1.0
ZN A:ZN801 3.9 42.4 1.0
O A:HOH944 4.1 25.3 1.0
CD2 A:HIS595 4.1 38.0 1.0
CD2 A:HIS567 4.2 41.2 1.0
OG1 A:THR633 4.2 40.2 1.0
CD2 A:HIS563 4.3 36.9 1.0
O A:THR633 4.3 42.7 1.0
NE2 A:HIS567 4.5 40.4 1.0
CB A:ASP564 4.5 33.6 1.0
CG A:GLU592 4.6 38.4 1.0
CD A:GLU592 4.6 38.7 1.0
CB A:THR633 4.7 39.5 1.0
O A:HIS563 4.7 35.9 1.0
NE2 A:HIS563 4.7 35.3 1.0
CA A:ASP564 4.8 35.6 1.0
NE2 A:HIS525 4.9 37.0 1.0
OD2 A:ASP674 4.9 37.8 1.0
CD2 A:HIS525 4.9 32.9 1.0
CE1 A:HIS595 4.9 40.2 1.0
C A:THR633 4.9 39.4 1.0

Magnesium binding site 2 out of 4 in 5skv

Go back to Magnesium Binding Sites List in 5skv
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.8
occ:1.00
 O B:HOH980 2.0 29.9 1.0
O B:HOH965 2.0 25.4 1.0
O B:HOH917 2.0 28.2 1.0
O B:HOH960 2.2 27.9 1.0
OD1 B:ASP564 2.3 33.3 1.0
CG B:ASP564 3.2 32.8 1.0
OD2 B:ASP564 3.5 31.9 1.0
ZN B:ZN801 3.8 35.0 1.0
O B:HOH1000 3.9 35.9 1.0
OE2 B:GLU592 3.9 30.9 1.0
NE2 B:HIS595 4.0 34.9 1.0
CD2 B:HIS563 4.0 31.6 1.0
CD2 B:HIS595 4.2 34.4 1.0
OG1 B:THR633 4.2 36.7 1.0
O B:HIS563 4.2 30.5 1.0
O B:THR633 4.3 31.7 1.0
CD2 B:HIS567 4.3 31.8 1.0
NE2 B:HIS567 4.4 30.8 1.0
NE2 B:HIS563 4.4 31.7 1.0
O B:HOH978 4.5 32.8 1.0
OD2 B:ASP674 4.5 35.1 1.0
CB B:THR633 4.5 31.0 1.0
CB B:ASP564 4.6 31.6 1.0
CD2 B:HIS525 4.6 29.0 1.0
CG B:GLU592 4.7 34.1 1.0
NE2 B:HIS525 4.7 29.5 1.0
CD B:GLU592 4.7 32.1 1.0
CA B:ASP564 4.8 33.2 1.0
C B:THR633 4.9 32.9 1.0

Magnesium binding site 3 out of 4 in 5skv

Go back to Magnesium Binding Sites List in 5skv
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:34.0
occ:1.00
 O C:HOH935 1.7 29.3 1.0
O C:HOH932 1.9 31.0 1.0
O C:HOH910 2.2 23.7 1.0
O C:HOH906 2.2 40.9 1.0
OD1 C:ASP564 2.3 28.4 1.0
O C:HOH954 2.4 28.9 1.0
CG C:ASP564 3.3 27.8 1.0
OD2 C:ASP564 3.5 28.5 1.0
ZN C:ZN801 3.7 38.4 1.0
O C:HOH1005 3.9 51.4 1.0
OE2 C:GLU592 4.1 34.0 1.0
OD2 C:ASP674 4.1 32.4 1.0
OG1 C:THR633 4.1 28.6 1.0
O C:THR633 4.2 32.7 1.0
CD2 C:HIS563 4.2 34.0 1.0
NE2 C:HIS595 4.4 36.9 1.0
NE2 C:HIS563 4.5 31.9 1.0
CD2 C:HIS567 4.6 36.3 1.0
CD2 C:HIS595 4.6 38.9 1.0
CB C:THR633 4.6 30.0 1.0
NE2 C:HIS567 4.6 37.7 1.0
CB C:ASP564 4.7 28.6 1.0
O C:HIS563 4.7 34.7 1.0
NE2 C:HIS525 4.7 34.9 1.0
CD2 C:HIS525 4.8 36.4 1.0
CG C:GLU592 4.8 36.2 1.0
CD C:GLU592 4.9 35.4 1.0
C C:THR633 4.9 33.5 1.0
OD1 C:ASP674 4.9 33.6 1.0
CG C:ASP674 4.9 32.0 1.0

Magnesium binding site 4 out of 4 in 5skv

Go back to Magnesium Binding Sites List in 5skv
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-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-[3-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]-1- Methylpyrazol-4-Yl]-3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:50.6
occ:1.00
 O D:HOH928 1.8 34.7 1.0
O D:HOH924 1.9 37.6 1.0
O D:HOH951 2.0 38.7 1.0
O D:HOH948 2.1 29.9 1.0
OD1 D:ASP564 2.3 38.4 1.0
O D:HOH919 2.3 30.4 1.0
CG D:ASP564 3.2 38.9 1.0
OD2 D:ASP564 3.4 39.4 1.0
ZN D:ZN801 3.8 43.0 1.0
OE2 D:GLU592 3.9 36.3 1.0
OG1 D:THR633 4.3 37.8 1.0
NE2 D:HIS595 4.3 40.5 1.0
OD2 D:ASP674 4.4 40.7 1.0
CD2 D:HIS567 4.4 42.2 1.0
CD2 D:HIS595 4.4 40.6 1.0
CD2 D:HIS563 4.5 37.4 1.0
O D:HIS563 4.5 39.8 1.0
O D:THR633 4.5 41.2 1.0
CB D:ASP564 4.5 39.1 1.0
NE2 D:HIS567 4.6 41.2 1.0
CD2 D:HIS525 4.6 42.2 1.0
NE2 D:HIS525 4.7 38.5 1.0
CB D:THR633 4.8 35.3 1.0
CD D:GLU592 4.8 35.8 1.0
CA D:ASP564 4.9 38.0 1.0
NE2 D:HIS563 4.9 36.3 1.0
CG D:GLU592 5.0 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: Tue Aug 12 20:20:35 2025

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