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Magnesium in PDB 5shi: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine, PDB code: 5shi was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.78 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.673, 135.673, 235.865, 90, 90, 120
R / Rfree (%) 17.4 / 22.3

Other elements in 5shi:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine (pdb code 5shi). 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine, PDB code: 5shi:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shi

Go back to Magnesium Binding Sites List in 5shi
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:30.8
occ:1.00
 O A:HOH1016 1.9 28.7 1.0
O A:HOH971 2.0 32.1 1.0
O A:HOH916 2.0 28.3 1.0
OD1 A:ASP564 2.0 29.6 1.0
O A:HOH937 2.1 31.0 1.0
O A:HOH956 2.3 31.0 1.0
CG A:ASP564 3.0 31.9 1.0
OD2 A:ASP564 3.4 37.8 1.0
ZN A:ZN802 3.8 38.3 1.0
O A:HOH993 3.9 39.3 1.0
O A:HOH1032 3.9 48.3 1.0
OE2 A:GLU592 4.1 36.1 1.0
NE2 A:HIS595 4.1 31.2 1.0
O A:HOH994 4.2 39.0 1.0
OG1 A:THR633 4.3 33.3 1.0
CD2 A:HIS567 4.4 35.6 1.0
O A:HIS563 4.4 32.2 1.0
CD2 A:HIS563 4.4 29.2 1.0
CB A:ASP564 4.4 30.0 1.0
CD2 A:HIS595 4.4 32.6 1.0
O A:THR633 4.4 32.4 1.0
OD2 A:ASP674 4.5 38.6 1.0
NE2 A:HIS567 4.6 33.7 1.0
CB A:THR633 4.6 31.9 1.0
CD2 A:HIS525 4.7 35.9 1.0
NE2 A:HIS525 4.7 35.7 1.0
NE2 A:HIS563 4.8 29.3 1.0
CA A:ASP564 4.8 33.2 1.0
CG A:GLU592 4.8 34.2 1.0
CD A:GLU592 4.9 35.2 1.0

Magnesium binding site 2 out of 4 in 5shi

Go back to Magnesium Binding Sites List in 5shi
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:29.5
occ:1.00
 O B:HOH961 1.9 27.7 1.0
O B:HOH940 2.0 33.1 1.0
O B:HOH921 2.0 26.9 1.0
OD1 B:ASP564 2.1 30.4 1.0
O B:HOH1005 2.1 29.8 1.0
O B:HOH982 2.2 25.3 1.0
CG B:ASP564 3.1 30.1 1.0
OD2 B:ASP564 3.5 32.2 1.0
O B:HOH1023 3.7 53.8 1.0
ZN B:ZN802 3.8 37.1 1.0
O B:HOH970 3.9 36.2 1.0
OE2 B:GLU592 4.0 34.0 1.0
NE2 B:HIS595 4.1 33.5 1.0
OG1 B:THR633 4.2 30.2 1.0
CD2 B:HIS563 4.2 30.9 1.0
O B:HIS563 4.3 31.1 1.0
O B:HOH979 4.3 31.8 1.0
CD2 B:HIS595 4.3 35.2 1.0
CD2 B:HIS567 4.4 34.6 1.0
OD2 B:ASP674 4.4 34.7 1.0
CB B:ASP564 4.5 29.4 1.0
NE2 B:HIS567 4.5 32.5 1.0
O B:THR633 4.5 32.1 1.0
NE2 B:HIS563 4.5 29.3 1.0
CB B:THR633 4.6 30.6 1.0
CD2 B:HIS525 4.6 30.5 1.0
NE2 B:HIS525 4.7 32.5 1.0
CG B:GLU592 4.7 35.3 1.0
CA B:ASP564 4.8 29.5 1.0
CD B:GLU592 4.8 34.1 1.0

Magnesium binding site 3 out of 4 in 5shi

Go back to Magnesium Binding Sites List in 5shi
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:31.7
occ:1.00
 O C:HOH942 2.0 28.2 1.0
O C:HOH975 2.0 31.0 1.0
O C:HOH949 2.0 30.5 1.0
OD1 C:ASP564 2.1 31.3 1.0
O C:HOH1020 2.1 30.3 1.0
O C:HOH930 2.2 28.2 1.0
CG C:ASP564 3.0 30.2 1.0
OD2 C:ASP564 3.3 30.4 1.0
ZN C:ZN802 3.7 37.4 1.0
O C:HOH1040 3.8 47.7 1.0
O C:HOH978 3.8 38.9 1.0
OE2 C:GLU592 4.0 33.3 1.0
NE2 C:HIS595 4.2 34.3 1.0
OG1 C:THR633 4.2 33.4 1.0
O C:HOH988 4.2 34.5 1.0
CD2 C:HIS563 4.2 31.0 1.0
CD2 C:HIS567 4.2 28.6 1.0
O C:HIS563 4.3 30.2 1.0
OD2 C:ASP674 4.4 39.2 1.0
CB C:ASP564 4.4 29.6 1.0
CD2 C:HIS595 4.4 32.2 1.0
NE2 C:HIS567 4.5 30.6 1.0
O C:THR633 4.5 32.5 1.0
NE2 C:HIS563 4.6 34.3 1.0
CD2 C:HIS525 4.7 35.6 1.0
CB C:THR633 4.7 31.3 1.0
NE2 C:HIS525 4.7 33.1 1.0
CA C:ASP564 4.8 31.7 1.0
CG C:GLU592 4.9 32.5 1.0
CD C:GLU592 4.9 34.3 1.0

Magnesium binding site 4 out of 4 in 5shi

Go back to Magnesium Binding Sites List in 5shi
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:45.0
occ:1.00
 O D:HOH963 2.0 37.1 1.0
O D:HOH930 2.1 37.4 1.0
O D:HOH915 2.1 38.6 1.0
O D:HOH951 2.1 40.2 1.0
OD1 D:ASP564 2.1 43.8 1.0
O D:HOH913 2.1 38.4 1.0
CG D:ASP564 3.2 43.6 1.0
OD2 D:ASP564 3.5 48.0 1.0
ZN D:ZN802 3.8 46.5 1.0
O D:HOH944 3.9 42.9 1.0
O D:HOH961 4.0 46.5 1.0
NE2 D:HIS595 4.0 44.2 1.0
OE2 D:GLU592 4.0 46.1 1.0
OG1 D:THR633 4.2 41.6 1.0
CD2 D:HIS567 4.3 45.2 1.0
CD2 D:HIS595 4.3 43.4 1.0
CD2 D:HIS563 4.3 38.0 1.0
O D:HIS563 4.4 43.2 1.0
O D:THR633 4.5 50.7 1.0
OD2 D:ASP674 4.5 46.9 1.0
CB D:ASP564 4.5 40.7 1.0
NE2 D:HIS567 4.5 44.5 1.0
CD2 D:HIS525 4.6 44.8 1.0
NE2 D:HIS525 4.6 49.3 1.0
NE2 D:HIS563 4.7 35.8 1.0
CB D:THR633 4.8 45.1 1.0
CG D:GLU592 4.8 47.9 1.0
CA D:ASP564 4.8 39.1 1.0
CD D:GLU592 4.9 49.3 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 04:00:11 2024

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