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Magnesium in PDB 5sjn: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sjn was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 2.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.272, 135.272, 235.07, 90, 90, 120
R / Rfree (%) 18.3 / 22.7

Other elements in 5sjn:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine also contains other interesting chemical elements:

Chlorine (Cl) 8 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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine (pdb code 5sjn). 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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sjn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjn

Go back to Magnesium Binding Sites List in 5sjn
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.2
occ:1.00
 O A:HOH991 2.0 27.3 1.0
OD1 A:ASP564 2.0 27.3 1.0
O A:HOH959 2.1 31.9 1.0
O A:HOH915 2.1 24.1 1.0
O A:HOH953 2.1 28.8 1.0
O A:HOH920 2.2 27.5 1.0
CG A:ASP564 3.0 29.2 1.0
OD2 A:ASP564 3.4 30.5 1.0
O A:HOH960 3.8 36.6 1.0
ZN A:ZN801 3.9 32.9 1.0
NE2 A:HIS595 3.9 30.3 1.0
OE2 A:GLU592 4.0 33.6 1.0
O A:HOH938 4.0 35.4 1.0
OG1 A:THR633 4.2 32.2 1.0
O A:HIS563 4.2 30.2 1.0
CD2 A:HIS567 4.3 27.9 1.0
CD2 A:HIS595 4.3 27.7 1.0
CD2 A:HIS563 4.4 27.5 1.0
CB A:ASP564 4.4 25.9 1.0
NE2 A:HIS567 4.5 29.6 1.0
CD2 A:HIS525 4.6 34.2 1.0
O A:THR633 4.6 30.2 1.0
NE2 A:HIS525 4.6 35.8 1.0
OD2 A:ASP674 4.7 33.6 1.0
CA A:ASP564 4.7 27.2 1.0
CB A:THR633 4.8 29.0 1.0
NE2 A:HIS563 4.8 27.3 1.0
CD A:GLU592 4.8 32.6 1.0
CG A:GLU592 4.8 27.9 1.0
CE1 A:HIS595 4.9 26.8 1.0

Magnesium binding site 2 out of 4 in 5sjn

Go back to Magnesium Binding Sites List in 5sjn
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.1
occ:1.00
 O B:HOH945 1.9 23.6 1.0
O B:HOH992 2.0 21.5 1.0
O B:HOH923 2.0 23.2 1.0
O B:HOH935 2.1 27.6 1.0
OD1 B:ASP564 2.1 25.8 1.0
O B:HOH963 2.2 23.0 1.0
CG B:ASP564 3.2 25.7 1.0
OD2 B:ASP564 3.5 25.3 1.0
ZN B:ZN801 3.7 31.4 1.0
O B:HOH952 3.8 41.5 1.0
OE2 B:GLU592 4.0 31.9 1.0
NE2 B:HIS595 4.1 29.6 1.0
O B:HOH938 4.2 36.3 1.0
CD2 B:HIS563 4.2 26.4 1.0
OG1 B:THR633 4.2 26.9 1.0
CD2 B:HIS567 4.3 28.1 1.0
OD2 B:ASP674 4.4 29.1 1.0
O B:HIS563 4.4 29.4 1.0
NE2 B:HIS567 4.5 26.6 1.0
NE2 B:HIS563 4.5 24.8 1.0
CD2 B:HIS595 4.5 29.4 1.0
CD2 B:HIS525 4.5 28.9 1.0
CB B:ASP564 4.5 25.9 1.0
O B:THR633 4.6 27.1 1.0
NE2 B:HIS525 4.6 31.5 1.0
CB B:THR633 4.6 26.7 1.0
CA B:ASP564 4.8 26.0 1.0
CD B:GLU592 4.9 31.1 1.0
CG B:GLU592 4.9 28.2 1.0

Magnesium binding site 3 out of 4 in 5sjn

Go back to Magnesium Binding Sites List in 5sjn
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.6
occ:1.00
 O C:HOH914 2.0 27.9 1.0
O C:HOH904 2.0 28.5 1.0
OD1 C:ASP564 2.1 28.3 1.0
O C:HOH909 2.2 26.7 1.0
O C:HOH994 2.2 28.6 1.0
O C:HOH954 2.2 25.5 1.0
CG C:ASP564 3.1 29.8 1.0
OD2 C:ASP564 3.5 30.2 1.0
ZN C:ZN801 3.7 33.5 1.0
O C:HOH1011 3.9 46.2 1.0
O C:HOH940 3.9 44.3 1.0
OE2 C:GLU592 4.0 32.2 1.0
NE2 C:HIS595 4.1 32.0 1.0
O C:HIS563 4.1 27.6 1.0
CD2 C:HIS563 4.2 24.6 1.0
CD2 C:HIS567 4.2 28.7 1.0
OG1 C:THR633 4.2 28.4 1.0
NE2 C:HIS567 4.4 30.2 1.0
OD2 C:ASP674 4.4 35.8 1.0
O C:HOH945 4.4 32.3 1.0
CD2 C:HIS595 4.4 28.2 1.0
O C:THR633 4.4 30.9 1.0
CB C:ASP564 4.5 25.1 1.0
CD2 C:HIS525 4.6 31.4 1.0
NE2 C:HIS563 4.6 27.5 1.0
CB C:THR633 4.6 27.3 1.0
NE2 C:HIS525 4.7 32.0 1.0
CA C:ASP564 4.7 28.5 1.0
CG C:GLU592 4.8 30.7 1.0
CD C:GLU592 4.9 33.5 1.0
C C:HIS563 5.0 27.2 1.0

Magnesium binding site 4 out of 4 in 5sjn

Go back to Magnesium Binding Sites List in 5sjn
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:35.1
occ:1.00
 O D:HOH941 2.0 36.2 1.0
O D:HOH940 2.0 29.5 1.0
O D:HOH922 2.1 34.7 1.0
OD1 D:ASP564 2.1 35.3 1.0
O D:HOH904 2.2 29.5 1.0
O D:HOH910 2.3 29.2 1.0
CG D:ASP564 3.2 34.1 1.0
OD2 D:ASP564 3.5 35.6 1.0
ZN D:ZN801 3.7 39.9 1.0
O D:HOH936 3.8 46.3 1.0
OE2 D:GLU592 4.0 39.4 1.0
NE2 D:HIS595 4.1 37.2 1.0
O D:HOH937 4.2 43.9 1.0
CD2 D:HIS567 4.2 37.0 1.0
OG1 D:THR633 4.2 34.0 1.0
CD2 D:HIS563 4.3 32.0 1.0
OD2 D:ASP674 4.4 39.1 1.0
CD2 D:HIS525 4.4 33.4 1.0
O D:HIS563 4.4 32.5 1.0
NE2 D:HIS567 4.5 37.0 1.0
CD2 D:HIS595 4.5 36.6 1.0
O D:THR633 4.5 43.9 1.0
NE2 D:HIS525 4.5 41.5 1.0
CB D:ASP564 4.5 30.6 1.0
CB D:THR633 4.7 37.2 1.0
NE2 D:HIS563 4.7 31.3 1.0
CA D:ASP564 4.9 31.4 1.0
CD D:GLU592 4.9 40.1 1.0
O D:HOH945 5.0 44.5 1.0
CG D:GLU592 5.0 41.2 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 04:24:16 2024

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