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Magnesium in PDB 5sgj: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide, PDB code: 5sgj was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.75 / 2.66
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.562, 135.562, 235.734, 90, 90, 120
R / Rfree (%) 18.2 / 26

Other elements in 5sgj:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide (pdb code 5sgj). 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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide, PDB code: 5sgj:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgj

Go back to Magnesium Binding Sites List in 5sgj
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.1
occ:1.00
 O A:HOH904 1.8 25.3 1.0
O A:HOH959 1.9 22.8 1.0
OD1 A:ASP564 2.0 31.6 1.0
O A:HOH942 2.0 19.7 1.0
O A:HOH943 2.2 22.0 1.0
O A:HOH926 2.4 23.4 1.0
CG A:ASP564 2.8 34.6 1.0
OD2 A:ASP564 3.0 34.6 1.0
ZN A:ZN801 3.7 38.7 1.0
O A:HOH945 4.0 33.0 1.0
OE2 A:GLU592 4.0 35.5 1.0
NE2 A:HIS595 4.1 35.2 1.0
CD2 A:HIS567 4.1 38.1 1.0
CB A:ASP564 4.2 36.8 1.0
CD2 A:HIS563 4.3 29.7 1.0
NE2 A:HIS567 4.3 40.1 1.0
OD2 A:ASP674 4.4 49.0 1.0
NE2 A:HIS525 4.4 32.4 1.0
CD2 A:HIS525 4.4 36.5 1.0
CD2 A:HIS595 4.5 28.8 1.0
NE2 A:HIS563 4.5 25.5 1.0
O A:HIS563 4.6 33.8 1.0
OG1 A:THR633 4.6 32.8 1.0
CA A:ASP564 4.7 37.8 1.0
CB A:THR633 4.9 30.0 1.0
O A:THR633 4.9 38.8 1.0
CD A:GLU592 5.0 37.6 1.0

Magnesium binding site 2 out of 4 in 5sgj

Go back to Magnesium Binding Sites List in 5sgj
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.9
occ:1.00
 O B:HOH961 1.8 24.6 1.0
O B:HOH909 1.8 23.3 1.0
O B:HOH916 1.9 23.3 1.0
O B:HOH941 2.0 14.5 1.0
O B:HOH907 2.0 26.4 1.0
OD1 B:ASP564 2.2 30.4 1.0
CG B:ASP564 3.2 30.6 1.0
OD2 B:ASP564 3.4 34.8 1.0
OE2 B:GLU592 3.8 38.2 1.0
ZN B:ZN801 3.8 39.0 1.0
O B:HOH910 4.1 27.7 1.0
CD2 B:HIS563 4.2 31.6 1.0
OG1 B:THR633 4.3 35.7 1.0
OD2 B:ASP674 4.3 45.0 1.0
NE2 B:HIS595 4.3 36.6 1.0
CD2 B:HIS567 4.4 29.5 1.0
O B:HIS563 4.5 30.6 1.0
NE2 B:HIS567 4.5 31.9 1.0
NE2 B:HIS563 4.5 30.4 1.0
O B:THR633 4.6 29.7 1.0
CB B:ASP564 4.6 29.8 1.0
CB B:THR633 4.6 31.0 1.0
CD2 B:HIS595 4.6 34.7 1.0
CD2 B:HIS525 4.6 35.2 1.0
CD B:GLU592 4.7 38.1 1.0
CG B:GLU592 4.8 35.9 1.0
NE2 B:HIS525 4.8 33.6 1.0
CA B:ASP564 5.0 29.7 1.0

Magnesium binding site 3 out of 4 in 5sgj

Go back to Magnesium Binding Sites List in 5sgj
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.6
occ:1.00
 O C:HOH932 1.8 23.1 1.0
O C:HOH924 1.8 35.2 1.0
O C:HOH908 2.1 28.0 1.0
OD1 C:ASP564 2.1 35.0 1.0
O C:HOH964 2.1 28.5 1.0
O C:HOH906 2.5 22.8 1.0
CG C:ASP564 3.0 33.4 1.0
OD2 C:ASP564 3.3 35.6 1.0
ZN C:ZN801 3.6 39.3 1.0
CD2 C:HIS563 4.1 30.2 1.0
OE2 C:GLU592 4.2 46.0 1.0
NE2 C:HIS595 4.3 39.1 1.0
NE2 C:HIS563 4.3 29.3 1.0
OD2 C:ASP674 4.3 40.5 1.0
CD2 C:HIS567 4.3 32.2 1.0
OG1 C:THR633 4.4 36.7 1.0
O C:THR633 4.4 40.9 1.0
CB C:ASP564 4.4 26.5 1.0
NE2 C:HIS567 4.4 33.6 1.0
O C:HIS563 4.5 29.7 1.0
CD2 C:HIS595 4.6 37.3 1.0
CD2 C:HIS525 4.6 45.8 1.0
NE2 C:HIS525 4.7 51.9 1.0
CB C:THR633 4.7 38.0 1.0
O C:HOH961 4.7 28.0 1.0
CA C:ASP564 4.8 28.4 1.0
OD1 C:ASP674 4.9 29.9 1.0

Magnesium binding site 4 out of 4 in 5sgj

Go back to Magnesium Binding Sites List in 5sgj
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-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 6-[(3, 6-Dimethylpyridine-2-Carbonyl)Amino]-N-Methyl-2-Phenyl-3H- Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:50.6
occ:1.00
 O D:HOH931 1.9 44.4 1.0
O D:HOH916 2.1 40.4 1.0
OD1 D:ASP564 2.1 33.7 1.0
O D:HOH906 2.2 26.9 1.0
O D:HOH909 2.4 34.2 1.0
CG D:ASP564 3.1 38.3 1.0
OD2 D:ASP564 3.4 43.3 1.0
O D:HOH919 3.4 36.3 1.0
ZN D:ZN801 3.7 49.6 1.0
CD2 D:HIS567 4.1 48.7 1.0
OE2 D:GLU592 4.1 41.7 1.0
NE2 D:HIS567 4.2 49.6 1.0
O D:HOH938 4.2 22.5 1.0
NE2 D:HIS595 4.3 49.2 1.0
OD2 D:ASP674 4.3 50.9 1.0
CD2 D:HIS563 4.3 34.5 1.0
CB D:ASP564 4.5 40.9 1.0
OG1 D:THR633 4.5 43.0 1.0
O D:THR633 4.6 48.0 1.0
NE2 D:HIS563 4.7 32.3 1.0
CD2 D:HIS525 4.7 52.4 1.0
CD2 D:HIS595 4.7 49.2 1.0
NE2 D:HIS525 4.7 54.5 1.0
O D:HIS563 4.8 43.8 1.0
CA D:ASP564 4.9 42.9 1.0
CB D:THR633 5.0 44.8 1.0
OD1 D:ASP674 5.0 47.0 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 19:39:47 2025

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