Atomistry » Magnesium » PDB 5sjc-5skf » 5sji
Atomistry »
  Magnesium »
    PDB 5sjc-5skf »
      5sji »

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

Go back to Magnesium Binding Sites List in 5sji
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

Go back to Magnesium Binding Sites List in 5sji
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

Go back to Magnesium Binding Sites List in 5sji
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: Tue Aug 12 20:07:25 2025

Last articles

Mg in 6ZZ6
Mg in 6ZYM
Mg in 6ZY9
Mg in 6ZY4
Mg in 6ZVH
Mg in 6ZXQ
Mg in 6ZXM
Mg in 6ZXA
Mg in 6ZXC
Mg in 6ZXF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy