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Magnesium in PDB 5sjt: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sjt was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.87 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.64, 134.64, 235, 90, 90, 120
R / Rfree (%) 16 / 17.9

Other elements in 5sjt:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide also contains other interesting chemical elements:

Praseodymium (Pr) 8 atoms
Zinc (Zn) 4 atoms
Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide (pdb code 5sjt). 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 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide, PDB code: 5sjt:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjt

Go back to Magnesium Binding Sites List in 5sjt
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.3
occ:1.00
 O A:HOH912 1.9 22.1 1.0
O A:HOH1006 1.9 22.8 1.0
O A:HOH993 1.9 27.8 1.0
OD1 A:ASP564 2.0 22.6 1.0
O A:HOH981 2.1 23.2 1.0
O A:HOH948 2.2 22.9 1.0
CG A:ASP564 3.1 24.9 1.0
OD2 A:ASP564 3.5 27.6 1.0
ZN A:ZN801 3.7 30.1 1.0
O A:HOH1005 3.9 23.1 1.0
NE2 A:HIS595 4.0 30.7 1.0
OE2 A:GLU592 4.1 30.0 1.0
O A:HIS563 4.2 25.2 1.0
OG1 A:THR633 4.3 27.6 1.0
CD2 A:HIS595 4.3 27.9 1.0
CD2 A:HIS567 4.3 30.4 1.0
CD2 A:HIS563 4.3 25.5 1.0
CB A:ASP564 4.4 23.6 1.0
NE2 A:HIS567 4.5 29.2 1.0
O A:THR633 4.5 29.3 1.0
OD2 A:ASP674 4.6 28.2 1.0
CD2 A:HIS525 4.6 29.2 1.0
NE2 A:HIS525 4.6 30.7 1.0
CB A:THR633 4.6 25.1 1.0
NE2 A:HIS563 4.6 25.6 1.0
CA A:ASP564 4.8 25.2 1.0
CG A:GLU592 4.8 27.7 1.0
O A:HOH1009 4.8 34.2 1.0
CD A:GLU592 4.9 28.4 1.0

Magnesium binding site 2 out of 4 in 5sjt

Go back to Magnesium Binding Sites List in 5sjt
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:20.6
occ:1.00
 O B:HOH912 1.8 25.2 1.0
O B:HOH1013 2.0 12.6 1.0
O B:HOH916 2.1 23.1 1.0
O B:HOH974 2.1 20.2 1.0
OD1 B:ASP564 2.1 25.4 1.0
O B:HOH913 2.1 20.0 1.0
CG B:ASP564 3.1 22.2 1.0
OD2 B:ASP564 3.4 21.9 1.0
ZN B:ZN801 3.8 26.3 1.0
OE2 B:GLU592 4.0 22.8 1.0
O B:HOH1004 4.0 32.1 1.0
NE2 B:HIS595 4.1 26.2 1.0
O B:HIS563 4.2 25.9 1.0
CD2 B:HIS567 4.2 23.4 1.0
OG1 B:THR633 4.2 24.1 1.0
CD2 B:HIS563 4.3 19.6 1.0
NE2 B:HIS567 4.3 26.3 1.0
O B:HOH1053 4.3 37.1 1.0
CD2 B:HIS595 4.3 28.0 1.0
O B:THR633 4.3 25.5 1.0
OD2 B:ASP674 4.4 23.9 1.0
O B:HOH1001 4.4 40.2 1.0
CB B:ASP564 4.5 21.1 1.0
NE2 B:HIS563 4.6 20.9 1.0
NE2 B:HIS525 4.6 23.9 1.0
CD2 B:HIS525 4.7 23.9 1.0
CG B:GLU592 4.7 25.1 1.0
CB B:THR633 4.7 25.9 1.0
CD B:GLU592 4.8 23.1 1.0
CA B:ASP564 4.8 22.9 1.0

Magnesium binding site 3 out of 4 in 5sjt

Go back to Magnesium Binding Sites List in 5sjt
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.6
occ:1.00
 O C:HOH1004 2.0 26.8 1.0
O C:HOH938 2.0 27.1 1.0
OD1 C:ASP564 2.0 21.5 1.0
O C:HOH915 2.1 17.5 1.0
O C:HOH960 2.1 23.5 1.0
O C:HOH930 2.2 20.8 1.0
CG C:ASP564 3.1 23.2 1.0
OD2 C:ASP564 3.4 23.3 1.0
ZN C:ZN801 3.7 30.3 1.0
O C:HOH934 3.9 50.5 1.0
NE2 C:HIS595 4.0 25.3 1.0
CD2 C:HIS567 4.1 27.7 1.0
O C:HIS563 4.1 23.2 1.0
NE2 C:HIS567 4.1 22.9 1.0
OE2 C:GLU592 4.2 31.0 1.0
CD2 C:HIS563 4.2 20.7 1.0
OG1 C:THR633 4.4 29.6 1.0
CB C:ASP564 4.4 23.0 1.0
CD2 C:HIS595 4.4 25.3 1.0
OD2 C:ASP674 4.4 31.3 1.0
CD2 C:HIS525 4.5 28.9 1.0
O C:THR633 4.5 28.0 1.0
O C:HOH995 4.5 45.0 1.0
NE2 C:HIS525 4.6 30.7 1.0
NE2 C:HIS563 4.6 22.4 1.0
CB C:THR633 4.6 27.1 1.0
CA C:ASP564 4.8 23.6 1.0
CG C:GLU592 4.9 28.8 1.0
CD C:GLU592 5.0 29.1 1.0

Magnesium binding site 4 out of 4 in 5sjt

Go back to Magnesium Binding Sites List in 5sjt
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide


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 4-N,4- N,2-Trimethyl-3-N-(2-Phenylimidazo[1,2-A]Pyridin-7-Yl)Pyrazole-3,4- Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.2
occ:1.00
 O D:HOH937 2.0 24.3 1.0
O D:HOH950 2.1 23.8 1.0
OD1 D:ASP564 2.1 27.7 1.0
O D:HOH949 2.1 24.9 1.0
O D:HOH922 2.1 32.9 1.0
O D:HOH923 2.4 30.7 1.0
CG D:ASP564 3.3 28.1 1.0
OD2 D:ASP564 3.7 31.8 1.0
OE2 D:GLU592 3.9 34.6 1.0
ZN D:ZN801 4.0 36.0 1.0
O D:HOH993 4.0 33.3 1.0
NE2 D:HIS595 4.1 33.0 1.0
CD2 D:HIS567 4.2 35.4 1.0
OG1 D:THR633 4.3 31.9 1.0
CD2 D:HIS595 4.3 34.1 1.0
O D:THR633 4.3 36.2 1.0
NE2 D:HIS567 4.4 36.4 1.0
O D:HOH958 4.4 38.2 1.0
CD2 D:HIS525 4.5 34.4 1.0
NE2 D:HIS525 4.5 32.5 1.0
O D:HIS563 4.6 29.4 1.0
CB D:ASP564 4.6 28.9 1.0
OD2 D:ASP674 4.6 28.1 1.0
CG D:GLU592 4.6 33.0 1.0
CD2 D:HIS563 4.7 29.2 1.0
CD D:GLU592 4.7 34.2 1.0
CA D:ASP564 4.8 29.6 1.0
CB D:THR633 4.8 32.7 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 04:27:05 2024

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