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Magnesium in PDB 5sh8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8 was solved by C.Joseph, J.Benz, A.Flohr, E.Vieira, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.54 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.51, 135.51, 235.29, 90, 90, 120
R / Rfree (%) 16 / 18.6

Other elements in 5sh8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide also contains other interesting chemical elements:

Praseodymium (Pr) 3 atoms
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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide (pdb code 5sh8). 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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:24.0
occ:1.00
 O A:HOH944 1.9 22.4 1.0
OD1 A:ASP564 1.9 24.8 1.0
O A:HOH1013 2.0 27.1 1.0
O A:HOH986 2.0 29.0 1.0
O A:HOH973 2.1 15.3 1.0
O A:HOH959 2.2 27.0 1.0
CG A:ASP564 3.0 24.6 1.0
OD2 A:ASP564 3.4 26.7 1.0
OE2 A:GLU592 3.8 33.3 1.0
ZN A:ZN802 3.9 30.2 1.0
NE2 A:HIS595 4.0 25.8 1.0
O A:HOH958 4.2 35.6 1.0
CD2 A:HIS563 4.2 23.7 1.0
CD2 A:HIS595 4.2 21.3 1.0
OG1 A:THR633 4.2 29.0 1.0
O A:HIS563 4.2 24.0 1.0
O A:HOH1001 4.3 30.9 1.0
CB A:ASP564 4.3 24.3 1.0
CD2 A:HIS567 4.3 32.0 1.0
NE2 A:HIS563 4.5 22.5 1.0
NE2 A:HIS567 4.6 27.7 1.0
CA A:ASP564 4.6 25.7 1.0
CD A:GLU592 4.7 30.7 1.0
CG A:GLU592 4.7 29.2 1.0
CB A:THR633 4.7 25.4 1.0
OD2 A:ASP674 4.7 31.4 1.0
O A:THR633 4.7 28.1 1.0
CD2 A:HIS525 4.8 27.8 1.0
C A:HIS563 4.9 23.8 1.0

Magnesium binding site 2 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:24.6
occ:1.00
 O B:HOH952 1.9 26.2 1.0
O B:HOH965 2.0 19.4 1.0
O B:HOH1013 2.0 22.3 1.0
O B:HOH1016 2.0 21.1 1.0
OD1 B:ASP564 2.1 23.4 1.0
O B:HOH948 2.2 26.4 1.0
CG B:ASP564 3.2 22.7 1.0
O B:HOH1006 3.6 44.7 1.0
OD2 B:ASP564 3.7 23.7 1.0
ZN B:ZN802 3.8 28.2 1.0
O B:HOH1025 3.9 38.7 1.0
NE2 B:HIS595 4.1 24.5 1.0
O B:HIS563 4.1 25.1 1.0
OE2 B:GLU592 4.1 27.9 1.0
CD2 B:HIS563 4.2 16.4 1.0
CD2 B:HIS595 4.2 24.8 1.0
OG1 B:THR633 4.2 24.0 1.0
CD2 B:HIS567 4.3 25.9 1.0
OD2 B:ASP674 4.4 25.6 1.0
CB B:ASP564 4.5 24.4 1.0
O B:HOH947 4.5 36.2 1.0
O B:THR633 4.5 27.6 1.0
NE2 B:HIS567 4.5 23.9 1.0
CA B:ASP564 4.6 23.3 1.0
CB B:THR633 4.7 26.1 1.0
NE2 B:HIS563 4.7 22.6 1.0
CD2 B:HIS525 4.8 26.1 1.0
NE2 B:HIS525 4.9 29.1 1.0
CG B:GLU592 4.9 27.3 1.0
C B:HIS563 4.9 23.6 1.0
CD B:GLU592 4.9 27.9 1.0

Magnesium binding site 3 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:21.7
occ:1.00
 O C:HOH981 2.0 26.1 1.0
O C:HOH952 2.1 31.9 1.0
OD1 C:ASP564 2.1 22.3 1.0
O C:HOH975 2.1 23.4 1.0
O C:HOH1008 2.1 20.7 1.0
O C:HOH908 2.2 26.1 1.0
CG C:ASP564 3.1 23.5 1.0
OD2 C:ASP564 3.5 21.4 1.0
ZN C:ZN802 3.8 31.8 1.0
O C:HOH979 3.9 41.1 1.0
NE2 C:HIS595 4.0 26.2 1.0
O C:HOH1025 4.0 42.8 1.0
OE2 C:GLU592 4.1 29.4 1.0
O C:HIS563 4.1 26.3 1.0
NE2 C:HIS567 4.2 31.6 1.0
OG1 C:THR633 4.2 28.2 1.0
CD2 C:HIS567 4.2 33.5 1.0
CD2 C:HIS563 4.3 26.7 1.0
CD2 C:HIS595 4.3 24.3 1.0
CB C:ASP564 4.4 27.6 1.0
OD2 C:ASP674 4.5 29.4 1.0
O C:HOH977 4.5 47.9 1.0
O C:THR633 4.6 31.8 1.0
NE2 C:HIS563 4.7 25.3 1.0
CD2 C:HIS525 4.7 27.2 1.0
CB C:THR633 4.7 27.2 1.0
CA C:ASP564 4.7 25.0 1.0
NE2 C:HIS525 4.8 32.2 1.0
CG C:GLU592 4.8 27.6 1.0
CD C:GLU592 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:26.6
occ:1.00
 O D:HOH1003 2.0 22.6 1.0
OD1 D:ASP564 2.1 25.4 1.0
O D:HOH918 2.1 34.4 1.0
O D:HOH935 2.1 22.9 1.0
O D:HOH943 2.1 24.4 1.0
O D:HOH971 2.2 20.9 1.0
CG D:ASP564 3.1 29.2 1.0
OD2 D:ASP564 3.5 34.0 1.0
ZN D:ZN802 3.8 33.2 1.0
O D:HOH946 3.9 31.4 1.0
OE2 D:GLU592 4.1 33.1 1.0
NE2 D:HIS595 4.2 29.5 1.0
CD2 D:HIS567 4.2 33.2 1.0
O D:HOH982 4.2 33.6 1.0
OG1 D:THR633 4.2 37.0 1.0
NE2 D:HIS567 4.3 27.1 1.0
CB D:ASP564 4.4 28.9 1.0
CD2 D:HIS595 4.5 30.9 1.0
O D:HIS563 4.6 31.1 1.0
CD2 D:HIS525 4.6 42.5 1.0
CD2 D:HIS563 4.6 32.3 1.0
OD2 D:ASP674 4.6 30.3 1.0
O D:THR633 4.7 41.0 1.0
CA D:ASP564 4.7 28.7 1.0
NE2 D:HIS525 4.8 36.2 1.0
CB D:THR633 4.8 38.2 1.0
NE2 D:HIS563 4.9 27.4 1.0
CG D:GLU592 4.9 34.5 1.0
CD D:GLU592 5.0 37.0 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: Wed Apr 5 11:23:57 2023

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