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Magnesium in PDB 5sh7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5sh7 was solved by C.Joseph, J.Benz, A.Flohr, K.Bleicher, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.66
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.448, 135.448, 236.063, 90, 90, 120
R / Rfree (%) 17.7 / 25.3

Other elements in 5sh7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide (pdb code 5sh7). 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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5sh7:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh7

Go back to Magnesium Binding Sites List in 5sh7
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:41.7
occ:1.00
 O A:HOH993 1.8 44.8 1.0
OD1 A:ASP564 2.0 34.4 1.0
O A:HOH938 2.1 34.1 1.0
O A:HOH924 2.2 37.7 1.0
O A:HOH922 2.4 39.6 1.0
O A:HOH931 2.4 33.0 1.0
CG A:ASP564 3.0 35.1 1.0
OD2 A:ASP564 3.4 41.8 1.0
O A:HOH907 3.7 30.7 1.0
O A:HOH937 3.8 37.7 1.0
ZN A:ZN801 3.8 40.5 1.0
CD2 A:HIS567 3.8 39.9 1.0
NE2 A:HIS595 3.9 38.7 1.0
NE2 A:HIS567 4.0 40.9 1.0
OE2 A:GLU592 4.3 35.3 1.0
CD2 A:HIS525 4.3 36.9 1.0
CD2 A:HIS595 4.3 35.7 1.0
CB A:ASP564 4.3 31.6 1.0
NE2 A:HIS525 4.4 35.9 1.0
O A:HIS563 4.4 38.0 1.0
CD2 A:HIS563 4.6 35.4 1.0
OG1 A:THR633 4.6 37.8 1.0
CA A:ASP564 4.7 38.1 1.0
OD2 A:ASP674 4.7 44.2 1.0
NE2 A:HIS563 4.7 29.9 1.0
O A:THR633 4.8 35.9 1.0
CG A:GLU592 5.0 34.6 1.0
CE1 A:HIS595 5.0 33.1 1.0

Magnesium binding site 2 out of 4 in 5sh7

Go back to Magnesium Binding Sites List in 5sh7
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:36.0
occ:1.00
 O B:HOH919 2.0 34.6 1.0
O B:HOH917 2.0 34.6 1.0
O B:HOH921 2.1 36.7 1.0
O B:HOH975 2.1 44.0 1.0
O B:HOH939 2.2 35.3 1.0
OD1 B:ASP564 2.5 36.5 1.0
O B:HOH928 3.2 42.7 1.0
CG B:ASP564 3.4 35.6 1.0
O B:HOH905 3.5 40.9 1.0
OD2 B:ASP564 3.6 38.0 1.0
CD2 B:HIS567 3.8 32.9 1.0
NE2 B:HIS567 3.8 35.7 1.0
ZN B:ZN801 4.0 39.8 1.0
NE2 B:HIS525 4.0 36.2 1.0
CD2 B:HIS525 4.1 39.9 1.0
NE2 B:HIS595 4.1 43.9 1.0
OE2 B:GLU592 4.2 39.1 1.0
CD2 B:HIS595 4.6 39.4 1.0
CD2 B:HIS563 4.8 34.9 1.0
CB B:ASP564 4.8 32.6 1.0
OD2 B:ASP674 4.9 41.8 1.0
NE2 B:HIS563 4.9 34.0 1.0
O B:THR633 5.0 34.4 1.0
O B:HOH932 5.0 43.4 1.0
CD B:GLU592 5.0 40.0 1.0

Magnesium binding site 3 out of 4 in 5sh7

Go back to Magnesium Binding Sites List in 5sh7
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:43.7
occ:1.00
 O C:HOH917 1.9 37.3 1.0
O C:HOH939 2.1 37.1 1.0
O C:HOH925 2.2 31.7 1.0
OD1 C:ASP564 2.3 42.5 1.0
O C:HOH911 2.4 38.5 1.0
O C:HOH959 2.5 44.3 1.0
CG C:ASP564 3.3 36.8 1.0
O C:HOH915 3.5 39.2 1.0
OD2 C:ASP564 3.5 38.9 1.0
ZN C:ZN801 3.8 41.8 1.0
CD2 C:HIS567 4.1 37.4 1.0
OE2 C:GLU592 4.1 40.6 1.0
NE2 C:HIS567 4.1 41.2 1.0
NE2 C:HIS525 4.2 36.9 1.0
NE2 C:HIS595 4.2 40.5 1.0
CD2 C:HIS525 4.3 41.9 1.0
O C:HOH977 4.3 45.8 1.0
OD2 C:ASP674 4.4 43.8 1.0
O C:THR633 4.5 41.1 1.0
O C:HOH1003 4.6 44.8 1.0
O C:HOH1014 4.6 46.9 1.0
CD2 C:HIS563 4.6 34.1 1.0
CD2 C:HIS595 4.6 40.4 1.0
CB C:ASP564 4.7 27.7 1.0
O C:HIS563 4.7 33.1 1.0
OG1 C:THR633 4.8 37.7 1.0
NE2 C:HIS563 4.9 33.3 1.0
CG C:GLU592 5.0 40.1 1.0

Magnesium binding site 4 out of 4 in 5sh7

Go back to Magnesium Binding Sites List in 5sh7
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-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-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:55.9
occ:1.00
 O D:HOH903 2.1 40.2 1.0
O D:HOH929 2.4 49.8 1.0
OD1 D:ASP564 2.4 47.9 1.0
O D:HOH926 2.7 40.7 1.0
O D:HOH958 2.9 52.4 1.0
O D:HOH936 3.1 49.2 1.0
CD2 D:HIS567 3.4 51.6 1.0
CG D:ASP564 3.5 47.0 1.0
NE2 D:HIS567 3.5 46.8 1.0
NE2 D:HIS595 3.6 49.2 1.0
OD2 D:ASP564 3.7 51.6 1.0
OE2 D:GLU592 3.8 53.8 1.0
CE1 D:HIS525 4.3 54.8 1.0
CD2 D:HIS595 4.3 46.7 1.0
ND1 D:HIS525 4.4 56.8 1.0
O D:HOH945 4.5 52.6 1.0
ZN D:ZN801 4.5 52.6 1.0
CE1 D:HIS595 4.6 51.6 1.0
CD D:GLU592 4.6 50.9 1.0
O D:HOH949 4.7 53.2 1.0
CG D:HIS567 4.7 51.2 1.0
CE1 D:HIS567 4.8 46.0 1.0
CB D:ASP564 4.8 44.3 1.0
O D:HIS563 4.9 46.8 1.0
CG D:GLU592 4.9 48.4 1.0
CB D:MET591 5.0 54.2 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 03:54:37 2024

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