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Magnesium in PDB 5sjw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjw 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) 43.67 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.122, 135.122, 235.325, 90, 90, 120
R / Rfree (%) 17.3 / 20.7

Other elements in 5sjw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide also contains other interesting chemical elements:

Chlorine (Cl) 5 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide (pdb code 5sjw). 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- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjw

Go back to Magnesium Binding Sites List in 5sjw
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.7
occ:1.00
 O A:HOH943 2.0 17.2 1.0
OD1 A:ASP564 2.0 18.8 1.0
O A:HOH1059 2.0 21.6 1.0
O A:HOH933 2.1 21.7 1.0
O A:HOH993 2.1 19.4 1.0
O A:HOH937 2.1 19.5 1.0
CG A:ASP564 3.0 19.8 1.0
OD2 A:ASP564 3.4 19.8 1.0
ZN A:ZN801 3.8 25.3 1.0
OE2 A:GLU592 4.0 25.1 1.0
NE2 A:HIS595 4.0 22.8 1.0
O A:HOH1036 4.0 27.5 1.0
O A:HOH1089 4.1 52.6 1.0
OG1 A:THR633 4.2 21.0 1.0
CD2 A:HIS563 4.2 19.4 1.0
CD2 A:HIS567 4.3 22.9 1.0
O A:HIS563 4.3 20.6 1.0
O A:HOH1019 4.3 28.4 1.0
CD2 A:HIS595 4.3 21.7 1.0
CB A:ASP564 4.4 19.6 1.0
OD2 A:ASP674 4.4 29.0 1.0
NE2 A:HIS567 4.5 22.4 1.0
O A:THR633 4.6 25.9 1.0
NE2 A:HIS563 4.6 20.1 1.0
CD2 A:HIS525 4.6 24.9 1.0
CB A:THR633 4.7 21.1 1.0
NE2 A:HIS525 4.7 25.2 1.0
CA A:ASP564 4.8 19.7 1.0
CG A:GLU592 4.8 22.9 1.0
CD A:GLU592 4.8 24.4 1.0

Magnesium binding site 2 out of 4 in 5sjw

Go back to Magnesium Binding Sites List in 5sjw
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:16.4
occ:1.00
 O B:HOH1062 2.0 20.6 1.0
O B:HOH985 2.0 16.1 1.0
O B:HOH1042 2.1 16.2 1.0
O B:HOH991 2.1 16.3 1.0
OD1 B:ASP564 2.1 18.9 1.0
O B:HOH917 2.1 15.8 1.0
CG B:ASP564 3.1 19.6 1.0
OD2 B:ASP564 3.4 18.2 1.0
ZN B:ZN801 3.8 23.8 1.0
O B:HOH1030 4.1 26.8 1.0
NE2 B:HIS595 4.1 22.9 1.0
OE2 B:GLU592 4.1 25.7 1.0
O B:HOH1076 4.2 47.2 1.0
CD2 B:HIS563 4.2 18.8 1.0
OG1 B:THR633 4.2 20.1 1.0
CD2 B:HIS567 4.3 20.7 1.0
OD2 B:ASP674 4.3 22.8 1.0
O B:HOH1031 4.3 25.8 1.0
O B:HIS563 4.3 21.9 1.0
CD2 B:HIS595 4.3 22.2 1.0
NE2 B:HIS567 4.4 19.7 1.0
CB B:ASP564 4.4 18.8 1.0
O B:THR633 4.5 19.2 1.0
NE2 B:HIS563 4.5 17.9 1.0
CD2 B:HIS525 4.6 22.9 1.0
NE2 B:HIS525 4.6 23.1 1.0
CB B:THR633 4.6 19.7 1.0
CA B:ASP564 4.8 19.5 1.0
CG B:GLU592 4.8 22.7 1.0
CD B:GLU592 4.9 23.1 1.0

Magnesium binding site 3 out of 4 in 5sjw

Go back to Magnesium Binding Sites List in 5sjw
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.5
occ:1.00
 OD1 C:ASP564 2.0 21.1 1.0
O C:HOH940 2.1 19.4 1.0
O C:HOH1048 2.1 22.1 1.0
O C:HOH1014 2.1 20.4 1.0
O C:HOH985 2.1 21.9 1.0
O C:HOH962 2.2 19.6 1.0
CG C:ASP564 3.1 21.2 1.0
OD2 C:ASP564 3.5 20.5 1.0
ZN C:ZN801 3.8 26.5 1.0
O C:HOH1009 4.0 27.6 1.0
NE2 C:HIS595 4.1 21.7 1.0
OE2 C:GLU592 4.1 25.4 1.0
CD2 C:HIS567 4.2 25.8 1.0
OG1 C:THR633 4.2 23.4 1.0
CD2 C:HIS563 4.3 19.5 1.0
O C:HOH1019 4.3 29.8 1.0
OD2 C:ASP674 4.3 29.2 1.0
O C:HIS563 4.3 21.3 1.0
O C:HOH1079 4.4 46.9 1.0
CD2 C:HIS595 4.4 21.2 1.0
NE2 C:HIS567 4.4 25.5 1.0
CB C:ASP564 4.4 19.4 1.0
O C:THR633 4.5 22.9 1.0
CD2 C:HIS525 4.6 26.3 1.0
NE2 C:HIS525 4.6 26.2 1.0
NE2 C:HIS563 4.7 19.3 1.0
CB C:THR633 4.7 22.7 1.0
CA C:ASP564 4.8 19.9 1.0
CG C:GLU592 4.8 22.4 1.0
CD C:GLU592 4.9 23.6 1.0

Magnesium binding site 4 out of 4 in 5sjw

Go back to Magnesium Binding Sites List in 5sjw
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.3
occ:1.00
 O D:HOH1033 2.0 28.4 1.0
O D:HOH1019 2.0 23.1 1.0
O D:HOH954 2.1 27.7 1.0
OD1 D:ASP564 2.1 28.4 1.0
O D:HOH924 2.1 21.4 1.0
O D:HOH929 2.2 29.5 1.0
CG D:ASP564 3.1 27.0 1.0
OD2 D:ASP564 3.5 28.4 1.0
ZN D:ZN801 3.8 32.2 1.0
NE2 D:HIS595 4.0 30.6 1.0
OE2 D:GLU592 4.0 33.2 1.0
O D:HOH959 4.1 33.8 1.0
O D:HOH1002 4.2 32.8 1.0
OG1 D:THR633 4.2 28.0 1.0
CD2 D:HIS567 4.2 33.6 1.0
CD2 D:HIS595 4.3 32.3 1.0
CD2 D:HIS563 4.3 25.1 1.0
O D:HIS563 4.4 28.8 1.0
OD2 D:ASP674 4.4 31.5 1.0
NE2 D:HIS567 4.4 31.6 1.0
O D:THR633 4.5 31.7 1.0
CB D:ASP564 4.5 26.6 1.0
CD2 D:HIS525 4.7 33.1 1.0
NE2 D:HIS563 4.7 23.7 1.0
NE2 D:HIS525 4.7 34.0 1.0
CB D:THR633 4.7 29.2 1.0
CG D:GLU592 4.8 31.8 1.0
CD D:GLU592 4.8 32.5 1.0
CA D:ASP564 4.8 26.8 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 04:27:09 2024

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