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Magnesium in PDB 5sk0: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5sk0 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) 43.91 / 2.02
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.679, 136.679, 236.402, 90, 90, 120
R / Rfree (%) 16.2 / 18.7

Other elements in 5sk0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide 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 N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide (pdb code 5sk0). 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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5sk0:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sk0

Go back to Magnesium Binding Sites List in 5sk0
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.4
occ:1.00
 O A:HOH917 2.0 31.1 1.0
O A:HOH1028 2.0 27.3 1.0
O A:HOH987 2.0 30.4 1.0
OD1 A:ASP564 2.0 28.8 1.0
O A:HOH982 2.1 27.6 1.0
O A:HOH936 2.2 28.4 1.0
CG A:ASP564 3.0 28.8 1.0
OD2 A:ASP564 3.3 33.6 1.0
O A:HOH927 3.8 35.4 1.0
ZN A:ZN801 3.8 31.7 1.0
OE2 A:GLU592 4.0 30.9 1.0
NE2 A:HIS595 4.1 29.1 1.0
O A:HOH1011 4.2 38.9 1.0
CD2 A:HIS567 4.3 35.4 1.0
OG1 A:THR633 4.3 28.6 1.0
CD2 A:HIS563 4.3 27.1 1.0
O A:HIS563 4.3 28.9 1.0
CB A:ASP564 4.4 34.6 1.0
CD2 A:HIS595 4.4 27.2 1.0
NE2 A:HIS567 4.4 37.1 1.0
O A:THR633 4.5 35.0 1.0
CD2 A:HIS525 4.6 35.4 1.0
OD2 A:ASP674 4.6 35.3 1.0
NE2 A:HIS563 4.7 29.9 1.0
NE2 A:HIS525 4.8 33.7 1.0
CA A:ASP564 4.8 30.8 1.0
CB A:THR633 4.8 32.1 1.0
CG A:GLU592 4.8 32.5 1.0
CD A:GLU592 4.9 33.0 1.0

Magnesium binding site 2 out of 4 in 5sk0

Go back to Magnesium Binding Sites List in 5sk0
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:27.6
occ:1.00
 O B:HOH957 2.0 23.3 1.0
O B:HOH1027 2.0 28.3 1.0
O B:HOH959 2.0 26.7 1.0
OD1 B:ASP564 2.0 25.0 1.0
O B:HOH1013 2.1 21.3 1.0
O B:HOH960 2.3 26.0 1.0
CG B:ASP564 3.0 24.6 1.0
OD2 B:ASP564 3.3 24.9 1.0
ZN B:ZN801 3.7 31.8 1.0
O B:HOH1052 3.8 40.4 1.0
O B:HOH949 3.9 42.2 1.0
CD2 B:HIS563 4.1 26.0 1.0
O B:HIS563 4.1 31.1 1.0
NE2 B:HIS595 4.1 30.1 1.0
OE2 B:GLU592 4.2 35.2 1.0
CD2 B:HIS567 4.2 36.3 1.0
OG1 B:THR633 4.3 27.9 1.0
CB B:ASP564 4.4 25.6 1.0
CD2 B:HIS595 4.4 30.2 1.0
NE2 B:HIS563 4.4 28.1 1.0
NE2 B:HIS567 4.4 31.3 1.0
OD2 B:ASP674 4.5 30.5 1.0
O B:HOH929 4.5 34.8 1.0
CA B:ASP564 4.6 25.0 1.0
CD2 B:HIS525 4.6 30.0 1.0
NE2 B:HIS525 4.6 30.9 1.0
CB B:THR633 4.7 29.1 1.0
O B:THR633 4.7 29.2 1.0
C B:HIS563 4.9 26.8 1.0

Magnesium binding site 3 out of 4 in 5sk0

Go back to Magnesium Binding Sites List in 5sk0
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.4
occ:1.00
 O C:HOH944 2.0 28.3 1.0
OD1 C:ASP564 2.0 24.2 1.0
O C:HOH1003 2.1 25.7 1.0
O C:HOH975 2.1 27.5 1.0
O C:HOH936 2.1 23.9 1.0
O C:HOH941 2.3 24.3 1.0
CG C:ASP564 3.1 23.3 1.0
OD2 C:ASP564 3.4 26.2 1.0
O C:HOH947 3.8 43.8 1.0
ZN C:ZN801 3.8 31.1 1.0
NE2 C:HIS595 4.0 28.3 1.0
OE2 C:GLU592 4.0 32.8 1.0
O C:HOH1006 4.1 45.3 1.0
CD2 C:HIS567 4.2 31.7 1.0
OG1 C:THR633 4.2 28.0 1.0
CD2 C:HIS563 4.2 26.3 1.0
CD2 C:HIS595 4.3 24.9 1.0
O C:HIS563 4.3 26.9 1.0
O C:HOH987 4.3 37.8 1.0
NE2 C:HIS567 4.4 30.8 1.0
OD2 C:ASP674 4.4 40.7 1.0
CB C:ASP564 4.4 23.1 1.0
CD2 C:HIS525 4.6 29.6 1.0
O C:THR633 4.6 29.4 1.0
NE2 C:HIS563 4.6 27.6 1.0
CB C:THR633 4.7 29.4 1.0
NE2 C:HIS525 4.7 33.1 1.0
CA C:ASP564 4.7 27.7 1.0
CG C:GLU592 4.8 25.5 1.0
CD C:GLU592 4.9 30.4 1.0
C C:HIS563 5.0 27.7 1.0

Magnesium binding site 4 out of 4 in 5sk0

Go back to Magnesium Binding Sites List in 5sk0
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-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- [(3R)-1-(5-Chloropyridin-2-Yl)Pyrrolidin-3-Yl]-1-Methyl-4-Pyridin-4- Ylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.0
occ:1.00
 OD1 D:ASP564 2.1 30.5 1.0
O D:HOH985 2.1 31.8 1.0
O D:HOH928 2.1 29.8 1.0
O D:HOH905 2.1 35.5 1.0
O D:HOH971 2.1 28.3 1.0
O D:HOH936 2.3 29.6 1.0
CG D:ASP564 3.0 30.7 1.0
OD2 D:ASP564 3.4 35.5 1.0
ZN D:ZN801 3.7 35.1 1.0
O D:HOH982 3.9 34.4 1.0
NE2 D:HIS595 4.0 31.6 1.0
O D:HOH976 4.0 45.9 1.0
OG1 D:THR633 4.1 35.8 1.0
CD2 D:HIS563 4.2 32.5 1.0
CD2 D:HIS595 4.2 35.5 1.0
CD2 D:HIS567 4.2 31.9 1.0
O D:HIS563 4.3 35.9 1.0
OE2 D:GLU592 4.3 40.1 1.0
NE2 D:HIS567 4.3 33.2 1.0
CB D:ASP564 4.4 30.0 1.0
OD2 D:ASP674 4.4 37.4 1.0
CD2 D:HIS525 4.5 32.6 1.0
NE2 D:HIS563 4.5 23.9 1.0
NE2 D:HIS525 4.6 50.9 1.0
CA D:ASP564 4.7 29.8 1.0
O D:THR633 4.7 35.9 1.0
CB D:THR633 4.7 34.4 1.0
CG D:GLU592 4.9 37.9 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 20:12:17 2025

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