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Magnesium in PDB 5shc: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide, PDB code: 5shc was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 2.33
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.409, 135.409, 234.936, 90, 90, 120
R / Rfree (%) 17.8 / 22.5

Other elements in 5shc:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide (pdb code 5shc). 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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide, PDB code: 5shc:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shc

Go back to Magnesium Binding Sites List in 5shc
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.7
occ:1.00
 O A:HOH961 1.9 32.7 1.0
OD1 A:ASP564 2.0 32.4 1.0
O A:HOH917 2.0 28.4 1.0
O A:HOH909 2.1 35.4 1.0
O A:HOH915 2.1 37.2 1.0
O A:HOH931 2.2 33.9 1.0
CG A:ASP564 3.0 34.5 1.0
OD2 A:ASP564 3.3 37.3 1.0
ZN A:ZN801 3.9 42.3 1.0
O A:HOH955 3.9 39.8 1.0
OE2 A:GLU592 4.0 45.9 1.0
NE2 A:HIS595 4.1 40.1 1.0
CD2 A:HIS567 4.2 43.1 1.0
O A:HOH945 4.2 48.3 1.0
CB A:ASP564 4.3 33.3 1.0
CD2 A:HIS563 4.4 34.1 1.0
O A:HIS563 4.4 41.9 1.0
CD2 A:HIS595 4.4 41.2 1.0
OG1 A:THR633 4.4 39.1 1.0
NE2 A:HIS567 4.4 43.8 1.0
OD2 A:ASP674 4.4 54.4 1.0
CD2 A:HIS525 4.5 40.6 1.0
O A:THR633 4.6 35.8 1.0
NE2 A:HIS525 4.6 41.5 1.0
NE2 A:HIS563 4.7 31.4 1.0
CB A:THR633 4.7 34.7 1.0
CA A:ASP564 4.8 36.2 1.0
CD A:GLU592 4.9 41.1 1.0
CG A:GLU592 4.9 37.5 1.0

Magnesium binding site 2 out of 4 in 5shc

Go back to Magnesium Binding Sites List in 5shc
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:34.3
occ:1.00
 O B:HOH924 1.8 33.8 1.0
O B:HOH948 2.0 33.9 1.0
O B:HOH929 2.0 26.7 1.0
O B:HOH968 2.1 31.6 1.0
O B:HOH908 2.1 28.8 1.0
OD1 B:ASP564 2.1 32.1 1.0
CG B:ASP564 3.1 35.0 1.0
OD2 B:ASP564 3.5 38.1 1.0
ZN B:ZN801 3.9 40.8 1.0
O B:HOH959 4.0 42.0 1.0
NE2 B:HIS595 4.0 41.9 1.0
OE2 B:GLU592 4.0 36.9 1.0
OG1 B:THR633 4.2 34.5 1.0
CD2 B:HIS563 4.2 33.5 1.0
O B:HOH938 4.3 37.5 1.0
CD2 B:HIS595 4.3 45.7 1.0
CD2 B:HIS567 4.3 36.1 1.0
OD2 B:ASP674 4.3 41.7 1.0
O B:HIS563 4.4 35.3 1.0
NE2 B:HIS567 4.5 38.6 1.0
CB B:ASP564 4.5 32.5 1.0
O B:THR633 4.5 37.1 1.0
NE2 B:HIS563 4.6 34.9 1.0
CB B:THR633 4.6 34.0 1.0
CD2 B:HIS525 4.7 42.2 1.0
CG B:GLU592 4.7 36.9 1.0
CA B:ASP564 4.8 35.5 1.0
NE2 B:HIS525 4.8 40.9 1.0
CD B:GLU592 4.8 35.9 1.0

Magnesium binding site 3 out of 4 in 5shc

Go back to Magnesium Binding Sites List in 5shc
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.6
occ:1.00
 O C:HOH934 2.0 36.1 1.0
O C:HOH928 2.1 28.1 1.0
O C:HOH951 2.1 33.7 1.0
O C:HOH966 2.1 35.5 1.0
OD1 C:ASP564 2.1 37.6 1.0
O C:HOH903 2.2 29.3 1.0
CG C:ASP564 3.1 36.1 1.0
OD2 C:ASP564 3.5 39.0 1.0
ZN C:ZN801 3.9 43.0 1.0
O C:HOH957 3.9 39.7 1.0
OE2 C:GLU592 4.0 39.4 1.0
NE2 C:HIS595 4.1 43.9 1.0
OG1 C:THR633 4.2 32.8 1.0
O C:HOH935 4.2 41.2 1.0
CD2 C:HIS563 4.2 33.1 1.0
CD2 C:HIS567 4.2 38.8 1.0
O C:HIS563 4.3 37.0 1.0
OD2 C:ASP674 4.3 37.5 1.0
CD2 C:HIS595 4.3 40.6 1.0
O C:THR633 4.5 36.8 1.0
NE2 C:HIS567 4.5 41.4 1.0
CB C:ASP564 4.5 35.5 1.0
CB C:THR633 4.7 35.3 1.0
NE2 C:HIS563 4.7 37.6 1.0
CG C:GLU592 4.8 40.0 1.0
CD C:GLU592 4.8 43.0 1.0
CD2 C:HIS525 4.8 38.7 1.0
NE2 C:HIS525 4.8 40.6 1.0
CA C:ASP564 4.8 36.4 1.0

Magnesium binding site 4 out of 4 in 5shc

Go back to Magnesium Binding Sites List in 5shc
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:54.3
occ:1.00
 O D:HOH910 2.1 36.9 1.0
O D:HOH918 2.1 46.8 1.0
O D:HOH903 2.2 43.9 1.0
OD1 D:ASP564 2.2 57.7 1.0
O D:HOH901 2.5 40.9 1.0
CG D:ASP564 3.1 56.1 1.0
OD2 D:ASP564 3.4 62.7 1.0
O D:HOH917 3.6 55.0 1.0
O D:HOH911 3.6 46.1 1.0
ZN D:ZN801 3.9 56.6 1.0
OE2 D:GLU592 3.9 56.5 1.0
CD2 D:HIS567 4.0 51.9 1.0
NE2 D:HIS595 4.1 55.6 1.0
NE2 D:HIS567 4.2 53.4 1.0
CD2 D:HIS525 4.3 62.6 1.0
NE2 D:HIS525 4.3 65.7 1.0
CD2 D:HIS595 4.4 52.7 1.0
OG1 D:THR633 4.5 48.1 1.0
CB D:ASP564 4.5 54.3 1.0
OD2 D:ASP674 4.6 61.0 1.0
CD2 D:HIS563 4.6 46.2 1.0
O D:HIS563 4.7 47.3 1.0
O D:THR633 4.7 49.7 1.0
NE2 D:HIS563 4.9 45.7 1.0
CA D:ASP564 4.9 52.5 1.0
CD D:GLU592 4.9 53.6 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 03:57:30 2024

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