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Magnesium in PDB 5sji: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-Methyl-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-Methyl-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-Methyl-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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide, PDB code: 5sji was solved by C.Joseph, J.Benz, A.Flohr, R.Canesso, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.42, 135.42, 235.47, 90, 90, 120
R / Rfree (%) 17.4 / 22.5

Other elements in 5sji:

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

Zinc (Zn) 4 atoms
Chlorine (Cl) 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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide (pdb code 5sji). 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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide, PDB code: 5sji:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sji

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

b:22.1
occ:1.00
 OD1 A:ASP564 2.0 19.4 1.0
O A:HOH984 2.0 22.7 1.0
O A:HOH916 2.0 17.8 1.0
O A:HOH1034 2.1 21.9 1.0
O A:HOH938 2.2 18.8 1.0
O A:HOH950 2.2 19.2 1.0
CG A:ASP564 3.0 22.8 1.0
OD2 A:ASP564 3.4 20.8 1.0
ZN A:ZN801 3.8 26.4 1.0
O A:HOH994 3.9 33.2 1.0
OE2 A:GLU592 4.0 24.4 1.0
NE2 A:HIS595 4.0 23.5 1.0
O A:HOH1009 4.1 24.7 1.0
OG1 A:THR633 4.3 22.1 1.0
CD2 A:HIS563 4.3 20.4 1.0
CB A:ASP564 4.4 21.2 1.0
O A:HIS563 4.4 24.0 1.0
CD2 A:HIS567 4.4 22.9 1.0
CD2 A:HIS595 4.4 20.5 1.0
O A:THR633 4.5 24.8 1.0
OD2 A:ASP674 4.5 26.1 1.0
CD2 A:HIS525 4.6 22.4 1.0
NE2 A:HIS525 4.6 24.6 1.0
NE2 A:HIS567 4.6 22.2 1.0
CB A:THR633 4.7 21.7 1.0
NE2 A:HIS563 4.7 21.9 1.0
CA A:ASP564 4.8 23.2 1.0
CG A:GLU592 4.8 23.0 1.0
CD A:GLU592 4.8 26.8 1.0

Magnesium binding site 2 out of 4 in 5sji

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

b:17.1
occ:1.00
 O B:HOH969 1.9 17.2 1.0
O B:HOH945 1.9 15.6 1.0
O B:HOH939 2.0 17.8 1.0
O B:HOH1041 2.1 18.4 1.0
OD1 B:ASP564 2.1 19.3 1.0
O B:HOH1022 2.1 15.0 1.0
CG B:ASP564 3.1 19.8 1.0
OD2 B:ASP564 3.5 20.5 1.0
ZN B:ZN801 3.7 24.8 1.0
O B:HOH984 3.9 37.6 1.0
O B:HOH1077 3.9 38.3 1.0
OE2 B:GLU592 4.0 25.1 1.0
NE2 B:HIS595 4.1 19.0 1.0
OG1 B:THR633 4.2 21.4 1.0
CD2 B:HIS563 4.2 17.7 1.0
O B:HIS563 4.3 22.6 1.0
O B:HOH1002 4.3 21.0 1.0
CD2 B:HIS595 4.3 21.4 1.0
CD2 B:HIS567 4.3 23.2 1.0
OD2 B:ASP674 4.4 19.3 1.0
CB B:ASP564 4.5 16.6 1.0
NE2 B:HIS567 4.5 20.3 1.0
O B:THR633 4.5 20.6 1.0
CB B:THR633 4.5 19.8 1.0
NE2 B:HIS563 4.6 17.7 1.0
CD2 B:HIS525 4.6 20.3 1.0
NE2 B:HIS525 4.6 22.1 1.0
CG B:GLU592 4.7 21.9 1.0
CA B:ASP564 4.7 17.7 1.0
CD B:GLU592 4.8 23.1 1.0

Magnesium binding site 3 out of 4 in 5sji

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

b:22.1
occ:1.00
 OD1 C:ASP564 2.0 18.5 1.0
O C:HOH943 2.0 18.1 1.0
O C:HOH947 2.1 23.1 1.0
O C:HOH950 2.1 20.7 1.0
O C:HOH991 2.1 19.1 1.0
O C:HOH1019 2.2 25.2 1.0
CG C:ASP564 3.0 20.3 1.0
OD2 C:ASP564 3.4 20.5 1.0
ZN C:ZN801 3.8 26.8 1.0
O C:HOH1065 3.9 45.5 1.0
OE2 C:GLU592 3.9 26.6 1.0
O C:HOH1011 3.9 44.3 1.0
NE2 C:HIS595 4.0 24.6 1.0
OG1 C:THR633 4.2 21.7 1.0
CD2 C:HIS567 4.2 21.9 1.0
CD2 C:HIS563 4.3 20.3 1.0
CD2 C:HIS595 4.3 23.5 1.0
O C:HIS563 4.3 21.9 1.0
CB C:ASP564 4.4 18.7 1.0
O C:HOH988 4.4 22.9 1.0
OD2 C:ASP674 4.4 29.8 1.0
O C:THR633 4.5 19.8 1.0
NE2 C:HIS567 4.5 20.9 1.0
CD2 C:HIS525 4.6 24.1 1.0
CB C:THR633 4.7 21.0 1.0
NE2 C:HIS525 4.7 22.8 1.0
CA C:ASP564 4.7 20.6 1.0
NE2 C:HIS563 4.8 23.1 1.0
CD C:GLU592 4.8 24.6 1.0
CG C:GLU592 4.8 22.0 1.0

Magnesium binding site 4 out of 4 in 5sji

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

b:31.2
occ:1.00
 O D:HOH993 2.0 20.2 1.0
OD1 D:ASP564 2.1 31.8 1.0
O D:HOH922 2.1 23.0 1.0
O D:HOH961 2.1 25.8 1.0
O D:HOH939 2.2 29.8 1.0
O D:HOH928 2.2 23.1 1.0
CG D:ASP564 3.1 29.2 1.0
OD2 D:ASP564 3.5 27.7 1.0
O D:HOH958 3.8 40.9 1.0
ZN D:ZN801 3.8 32.7 1.0
NE2 D:HIS595 4.0 27.7 1.0
OE2 D:GLU592 4.0 29.0 1.0
O D:HOH985 4.0 30.6 1.0
OG1 D:THR633 4.2 26.4 1.0
CD2 D:HIS567 4.3 31.9 1.0
CD2 D:HIS595 4.3 28.5 1.0
CD2 D:HIS563 4.3 24.6 1.0
O D:HIS563 4.4 27.5 1.0
O D:THR633 4.4 31.5 1.0
NE2 D:HIS525 4.4 36.0 1.0
OD2 D:ASP674 4.4 29.1 1.0
NE2 D:HIS567 4.5 29.0 1.0
CB D:ASP564 4.5 26.9 1.0
CD2 D:HIS525 4.5 32.7 1.0
NE2 D:HIS563 4.7 25.7 1.0
CB D:THR633 4.7 29.4 1.0
CA D:ASP564 4.8 27.9 1.0
CD D:GLU592 4.9 34.9 1.0
CG D:GLU592 4.9 33.9 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 04:22:19 2024

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