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Magnesium in PDB 5skc: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-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-(1-Propan-2-Ylpyrazol-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-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5skc 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) 43.87 / 2.60
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.69, 136.69, 236.14, 90, 90, 120
R / Rfree (%) 21.6 / 24.2

Other elements in 5skc:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-3-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- Methyl-N-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide (pdb code 5skc). 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-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide, PDB code: 5skc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skc

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

b:47.7
occ:1.00
 O A:HOH907 2.1 43.1 1.0
O A:HOH925 2.1 61.3 1.0
OD1 A:ASP564 2.4 56.3 1.0
O A:HOH912 2.5 65.0 1.0
O A:HOH902 2.6 72.7 1.0
CG A:ASP564 3.3 56.7 1.0
O A:HOH908 3.5 64.7 1.0
OD2 A:ASP564 3.5 61.4 1.0
ZN A:ZN801 3.6 59.4 1.0
OE2 A:GLU592 3.8 70.2 1.0
O A:HOH929 3.8 61.0 1.0
OG1 A:THR633 4.0 55.8 1.0
O A:THR633 4.1 52.9 1.0
CD2 A:HIS563 4.1 49.5 1.0
OD2 A:ASP674 4.2 66.4 1.0
CB A:THR633 4.3 54.1 1.0
NE2 A:HIS595 4.4 58.7 1.0
O A:HIS563 4.5 50.1 1.0
NE2 A:HIS563 4.6 50.4 1.0
NE2 A:HIS525 4.6 51.8 1.0
CD2 A:HIS525 4.6 51.0 1.0
CD2 A:HIS595 4.6 57.4 1.0
CB A:ASP564 4.7 50.8 1.0
CD2 A:HIS567 4.8 58.1 1.0
C A:THR633 4.8 53.0 1.0
CD A:GLU592 4.8 67.1 1.0
OD1 A:ASP674 4.8 63.9 1.0
CG A:ASP674 4.9 63.4 1.0
CG A:GLU592 4.9 62.5 1.0
NE2 A:HIS567 4.9 59.5 1.0

Magnesium binding site 2 out of 4 in 5skc

Go back to Magnesium Binding Sites List in 5skc
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(1-Propan-2-Ylpyrazol-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-(1-Propan-2-Ylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino)Pyridine- 2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:41.4
occ:1.00
 O B:HOH916 2.0 54.1 1.0
O B:HOH920 2.1 52.9 1.0
OD1 B:ASP564 2.1 47.9 1.0
O B:HOH918 2.2 58.8 1.0
O B:HOH933 2.3 53.5 1.0
O B:HOH928 2.3 40.9 1.0
CG B:ASP564 3.1 46.8 1.0
OD2 B:ASP564 3.3 46.8 1.0
ZN B:ZN801 3.5 54.5 1.0
O B:HOH935 3.9 56.8 1.0
CD2 B:HIS563 4.0 46.9 1.0
OG1 B:THR633 4.3 53.9 1.0
OD2 B:ASP674 4.3 60.4 1.0
CD2 B:HIS525 4.4 53.0 1.0
NE2 B:HIS525 4.4 53.8 1.0
NE2 B:HIS595 4.4 56.7 1.0
CB B:ASP564 4.4 45.3 1.0
OE2 B:GLU592 4.5 57.1 1.0
CD2 B:HIS567 4.5 61.3 1.0
O B:HIS563 4.5 47.5 1.0
NE2 B:HIS563 4.5 48.5 1.0
O B:THR633 4.6 52.8 1.0
CD2 B:HIS595 4.6 55.9 1.0
NE2 B:HIS567 4.6 62.6 1.0
CB B:THR633 4.7 53.2 1.0
OD1 B:ASP674 4.8 56.8 1.0
CA B:ASP564 4.8 46.5 1.0
CG B:ASP674 5.0 56.5 1.0

Magnesium binding site 3 out of 4 in 5skc

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

b:40.6
occ:1.00
 O C:HOH906 2.1 44.4 1.0
O C:HOH910 2.2 48.7 1.0
O C:HOH903 2.2 57.4 1.0
OD1 C:ASP564 2.3 53.9 1.0
O C:HOH926 2.3 44.5 1.0
O C:HOH929 2.3 49.7 1.0
CG C:ASP564 3.2 53.2 1.0
OD2 C:ASP564 3.4 56.1 1.0
ZN C:ZN801 3.8 57.6 1.0
O C:HOH921 3.9 90.1 1.0
OE2 C:GLU592 4.1 58.5 1.0
CD2 C:HIS563 4.1 41.3 1.0
NE2 C:HIS595 4.1 56.5 1.0
OG1 C:THR633 4.2 49.8 1.0
CD2 C:HIS595 4.3 55.7 1.0
O C:HIS563 4.4 43.9 1.0
CD2 C:HIS567 4.4 54.0 1.0
NE2 C:HIS563 4.4 42.9 1.0
OD2 C:ASP674 4.4 57.2 1.0
O C:THR633 4.5 48.7 1.0
CD2 C:HIS525 4.5 53.3 1.0
CB C:ASP564 4.5 48.2 1.0
NE2 C:HIS567 4.5 54.9 1.0
NE2 C:HIS525 4.6 54.2 1.0
CB C:THR633 4.6 48.7 1.0
CA C:ASP564 4.8 46.8 1.0
CG C:GLU592 4.9 55.2 1.0
CD C:GLU592 5.0 59.2 1.0

Magnesium binding site 4 out of 4 in 5skc

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

b:101.1
occ:1.00
 O D:HOH908 2.1 57.3 1.0
O D:HOH905 2.1 64.0 1.0
OD1 D:ASP564 2.8 74.8 1.0
O D:HOH902 2.8 51.2 1.0
OE2 D:GLU592 2.9 89.3 1.0
O D:HOH906 3.0 94.4 1.0
NE2 D:HIS595 3.4 76.7 1.0
CD2 D:HIS595 3.7 75.5 1.0
CD D:GLU592 3.8 85.6 1.0
CD2 D:HIS567 3.9 85.6 1.0
NE2 D:HIS567 3.9 86.7 1.0
CG D:ASP564 4.0 75.6 1.0
CG D:GLU592 4.3 82.3 1.0
OD2 D:ASP564 4.5 78.4 1.0
CB D:MET591 4.6 84.9 1.0
O D:HIS563 4.6 69.1 1.0
CE1 D:HIS595 4.6 76.5 1.0
OG1 D:THR633 4.7 81.7 1.0
O D:HOH910 4.8 80.4 1.0
O D:THR633 4.8 81.8 1.0
OE1 D:GLU592 4.8 83.1 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 04:32:57 2024

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