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Magnesium in PDB 5skr: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-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 1- Methyl-N-(2-Methyl-5-Pyridin-2-Ylpyrazol-3-Yl)-4-Pyridin-4- Ylpyrazole-3-Carboxamide, PDB code: 5skr 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) 43.59 / 1.99
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.501, 135.501, 235.242, 90, 90, 120
R / Rfree (%) 17.9 / 21.9

Other elements in 5skr:

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

Magnesium binding site 1 out of 4 in 5skr

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

b:25.8
occ:1.00
 O A:HOH931 2.0 24.3 1.0
O A:HOH1019 2.0 25.5 1.0
OD1 A:ASP564 2.0 26.6 1.0
O A:HOH922 2.0 22.7 1.0
O A:HOH967 2.1 20.8 1.0
O A:HOH947 2.2 25.7 1.0
CG A:ASP564 3.0 27.9 1.0
OD2 A:ASP564 3.3 28.1 1.0
ZN A:ZN801 3.8 30.8 1.0
O A:HOH1010 4.0 35.7 1.0
OE2 A:GLU592 4.0 32.1 1.0
NE2 A:HIS595 4.1 29.7 1.0
OG1 A:THR633 4.2 27.3 1.0
CD2 A:HIS595 4.3 26.4 1.0
CD2 A:HIS563 4.3 24.6 1.0
CD2 A:HIS567 4.3 31.9 1.0
O A:HIS563 4.3 28.1 1.0
CB A:ASP564 4.3 28.3 1.0
OD2 A:ASP674 4.4 36.5 1.0
NE2 A:HIS567 4.5 30.0 1.0
O A:HOH975 4.5 38.9 1.0
O A:THR633 4.5 29.1 1.0
CD2 A:HIS525 4.6 32.0 1.0
NE2 A:HIS563 4.7 28.4 1.0
NE2 A:HIS525 4.7 30.4 1.0
CB A:THR633 4.7 29.1 1.0
CA A:ASP564 4.8 27.1 1.0
CG A:GLU592 4.8 28.0 1.0
CD A:GLU592 4.8 29.8 1.0

Magnesium binding site 2 out of 4 in 5skr

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

b:25.6
occ:1.00
 O B:HOH937 1.9 24.3 1.0
O B:HOH930 2.0 19.8 1.0
OD1 B:ASP564 2.0 25.6 1.0
O B:HOH957 2.1 23.1 1.0
O B:HOH1011 2.1 26.9 1.0
O B:HOH992 2.1 21.2 1.0
CG B:ASP564 3.0 22.9 1.0
OD2 B:ASP564 3.4 24.1 1.0
ZN B:ZN801 3.7 29.4 1.0
O B:HOH1046 3.9 49.5 1.0
O B:HOH985 4.0 35.3 1.0
NE2 B:HIS595 4.1 24.8 1.0
OE2 B:GLU592 4.1 30.4 1.0
OG1 B:THR633 4.2 25.0 1.0
CD2 B:HIS563 4.2 22.5 1.0
OD2 B:ASP674 4.3 28.7 1.0
CD2 B:HIS567 4.3 28.6 1.0
O B:HIS563 4.3 26.8 1.0
O B:HOH966 4.3 31.5 1.0
CD2 B:HIS595 4.3 25.4 1.0
CB B:ASP564 4.4 25.9 1.0
NE2 B:HIS567 4.4 22.4 1.0
O B:THR633 4.6 25.7 1.0
CD2 B:HIS525 4.6 27.9 1.0
NE2 B:HIS563 4.6 20.4 1.0
CB B:THR633 4.6 26.7 1.0
NE2 B:HIS525 4.6 27.2 1.0
CA B:ASP564 4.7 24.2 1.0
CG B:GLU592 4.7 29.6 1.0
CD B:GLU592 4.9 27.7 1.0

Magnesium binding site 3 out of 4 in 5skr

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

b:25.9
occ:1.00
 O C:HOH933 2.0 29.4 1.0
O C:HOH1025 2.0 23.5 1.0
O C:HOH1003 2.1 23.3 1.0
O C:HOH938 2.1 24.5 1.0
O C:HOH951 2.1 24.0 1.0
OD1 C:ASP564 2.1 25.8 1.0
CG C:ASP564 3.2 28.6 1.0
OD2 C:ASP564 3.6 28.5 1.0
ZN C:ZN801 3.8 32.6 1.0
O C:HOH1021 4.0 38.0 1.0
OE2 C:GLU592 4.0 33.5 1.0
NE2 C:HIS595 4.1 26.2 1.0
CD2 C:HIS567 4.2 29.0 1.0
O C:HOH988 4.2 36.2 1.0
NE2 C:HIS567 4.2 30.1 1.0
CD2 C:HIS563 4.3 24.6 1.0
OG1 C:THR633 4.3 30.6 1.0
OD2 C:ASP674 4.4 34.5 1.0
O C:HIS563 4.4 27.9 1.0
CD2 C:HIS595 4.4 23.8 1.0
CB C:ASP564 4.6 25.3 1.0
O C:THR633 4.6 29.6 1.0
NE2 C:HIS563 4.6 26.0 1.0
CD2 C:HIS525 4.7 36.6 1.0
NE2 C:HIS525 4.7 34.8 1.0
CB C:THR633 4.7 28.8 1.0
CD C:GLU592 4.8 29.1 1.0
CG C:GLU592 4.8 25.1 1.0
CA C:ASP564 4.9 25.7 1.0

Magnesium binding site 4 out of 4 in 5skr

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

b:31.7
occ:1.00
 O D:HOH992 2.0 31.1 1.0
O D:HOH967 2.0 24.0 1.0
OD1 D:ASP564 2.0 29.9 1.0
O D:HOH922 2.1 26.4 1.0
O D:HOH951 2.1 27.6 1.0
O D:HOH921 2.1 27.8 1.0
CG D:ASP564 3.1 30.2 1.0
OD2 D:ASP564 3.4 28.8 1.0
ZN D:ZN801 3.8 35.4 1.0
O D:HOH968 4.0 35.8 1.0
NE2 D:HIS595 4.0 32.7 1.0
OG1 D:THR633 4.2 31.5 1.0
OE2 D:GLU592 4.2 38.7 1.0
O D:HOH977 4.2 39.5 1.0
CD2 D:HIS567 4.3 40.6 1.0
CD2 D:HIS563 4.3 32.3 1.0
O D:HIS563 4.3 31.0 1.0
CD2 D:HIS595 4.3 34.8 1.0
OD2 D:ASP674 4.4 33.4 1.0
CB D:ASP564 4.4 30.3 1.0
O D:THR633 4.5 38.2 1.0
NE2 D:HIS567 4.5 36.8 1.0
CD2 D:HIS525 4.6 40.2 1.0
NE2 D:HIS525 4.7 37.4 1.0
NE2 D:HIS563 4.7 28.1 1.0
CB D:THR633 4.7 30.8 1.0
CA D:ASP564 4.7 27.6 1.0
CG D:GLU592 4.9 36.3 1.0
CD D:GLU592 5.0 36.4 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 04:37:45 2024

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