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Magnesium in PDB 5sfz: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-3-(2-Phenylpyrazol-3-Yl) Urea

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]-3-(2-Phenylpyrazol-3-Yl) Urea:
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]-3-(2-Phenylpyrazol-3-Yl) Urea, PDB code: 5sfz 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) 43.49 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.195, 135.195, 234.845, 90, 90, 120
R / Rfree (%) 19.1 / 23.5

Other elements in 5sfz:

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

Magnesium binding site 1 out of 4 in 5sfz

Go back to Magnesium Binding Sites List in 5sfz
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]-3-(2-Phenylpyrazol-3-Yl) Urea


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]-3-(2-Phenylpyrazol-3-Yl) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.9
occ:1.00
 O A:HOH1004 2.0 23.9 1.0
O A:HOH953 2.0 22.4 1.0
O A:HOH955 2.0 21.6 1.0
O A:HOH934 2.0 25.6 1.0
OD1 A:ASP564 2.0 23.3 1.0
O A:HOH920 2.2 26.3 1.0
CG A:ASP564 3.1 24.7 1.0
OD2 A:ASP564 3.5 26.8 1.0
ZN A:ZN801 3.8 30.5 1.0
OE2 A:GLU592 4.0 31.2 1.0
NE2 A:HIS595 4.0 28.6 1.0
O A:HOH970 4.0 30.2 1.0
O A:HOH1010 4.1 49.8 1.0
CD2 A:HIS567 4.1 31.4 1.0
O A:HOH951 4.2 29.0 1.0
OG1 A:THR633 4.3 28.9 1.0
CD2 A:HIS595 4.3 29.0 1.0
NE2 A:HIS567 4.4 29.3 1.0
CD2 A:HIS563 4.4 26.8 1.0
O A:THR633 4.4 30.2 1.0
CB A:ASP564 4.4 24.7 1.0
O A:HIS563 4.4 26.0 1.0
OD2 A:ASP674 4.5 34.1 1.0
NE2 A:HIS525 4.6 27.4 1.0
CD2 A:HIS525 4.6 29.0 1.0
NE2 A:HIS563 4.8 26.3 1.0
CB A:THR633 4.8 28.1 1.0
CD A:GLU592 4.8 30.7 1.0
CG A:GLU592 4.8 27.9 1.0
CA A:ASP564 4.8 25.9 1.0

Magnesium binding site 2 out of 4 in 5sfz

Go back to Magnesium Binding Sites List in 5sfz
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]-3-(2-Phenylpyrazol-3-Yl) Urea


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]-3-(2-Phenylpyrazol-3-Yl) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.9
occ:1.00
 O B:HOH953 2.0 20.6 1.0
O B:HOH947 2.0 20.7 1.0
O B:HOH906 2.1 22.7 1.0
O B:HOH979 2.1 22.2 1.0
OD1 B:ASP564 2.1 24.6 1.0
O B:HOH980 2.1 19.8 1.0
CG B:ASP564 3.1 23.9 1.0
OD2 B:ASP564 3.5 24.9 1.0
ZN B:ZN801 3.8 29.7 1.0
OE2 B:GLU592 4.0 30.0 1.0
O B:HOH971 4.0 32.1 1.0
NE2 B:HIS595 4.1 27.1 1.0
OG1 B:THR633 4.2 25.6 1.0
CD2 B:HIS563 4.2 23.6 1.0
O B:HOH992 4.3 33.8 1.0
O B:HIS563 4.3 26.6 1.0
OD2 B:ASP674 4.3 28.3 1.0
CD2 B:HIS567 4.3 25.0 1.0
CD2 B:HIS595 4.4 29.4 1.0
O B:THR633 4.4 28.0 1.0
NE2 B:HIS567 4.5 24.8 1.0
CB B:ASP564 4.5 23.7 1.0
NE2 B:HIS563 4.6 23.7 1.0
CD2 B:HIS525 4.6 24.5 1.0
NE2 B:HIS525 4.6 24.4 1.0
CB B:THR633 4.6 25.7 1.0
CG B:GLU592 4.8 30.1 1.0
CA B:ASP564 4.8 24.3 1.0
CD B:GLU592 4.8 28.5 1.0

Magnesium binding site 3 out of 4 in 5sfz

Go back to Magnesium Binding Sites List in 5sfz
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]-3-(2-Phenylpyrazol-3-Yl) Urea


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]-3-(2-Phenylpyrazol-3-Yl) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.6
occ:1.00
 O C:HOH985 2.0 25.7 1.0
O C:HOH951 2.0 26.8 1.0
O C:HOH1022 2.0 25.5 1.0
O C:HOH968 2.1 26.0 1.0
OD1 C:ASP564 2.1 26.3 1.0
O C:HOH930 2.2 21.6 1.0
CG C:ASP564 3.1 27.1 1.0
OD2 C:ASP564 3.4 28.8 1.0
ZN C:ZN801 3.7 32.7 1.0
O C:HOH994 3.9 27.8 1.0
NE2 C:HIS595 4.1 28.6 1.0
OE2 C:GLU592 4.2 31.5 1.0
CD2 C:HIS567 4.2 28.1 1.0
O C:HOH991 4.2 29.9 1.0
OG1 C:THR633 4.3 26.5 1.0
CD2 C:HIS563 4.3 23.8 1.0
NE2 C:HIS567 4.3 26.1 1.0
O C:HIS563 4.4 26.4 1.0
OD2 C:ASP674 4.4 28.0 1.0
CD2 C:HIS595 4.4 27.7 1.0
O C:THR633 4.4 28.7 1.0
CB C:ASP564 4.5 24.7 1.0
CD2 C:HIS525 4.6 29.4 1.0
NE2 C:HIS563 4.7 25.8 1.0
CB C:THR633 4.7 27.4 1.0
NE2 C:HIS525 4.7 29.8 1.0
CA C:ASP564 4.8 25.5 1.0
CG C:GLU592 4.9 27.9 1.0
CD C:GLU592 5.0 28.8 1.0

Magnesium binding site 4 out of 4 in 5sfz

Go back to Magnesium Binding Sites List in 5sfz
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]-3-(2-Phenylpyrazol-3-Yl) Urea


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]-3-(2-Phenylpyrazol-3-Yl) Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.5
occ:1.00
 O D:HOH920 2.1 33.1 1.0
O D:HOH936 2.1 25.2 1.0
O D:HOH958 2.1 25.6 1.0
O D:HOH951 2.1 32.1 1.0
O D:HOH903 2.2 32.0 1.0
OD1 D:ASP564 2.2 34.0 1.0
CG D:ASP564 3.2 32.2 1.0
OD2 D:ASP564 3.5 39.0 1.0
ZN D:ZN801 3.8 40.1 1.0
O D:HOH956 3.9 33.0 1.0
O D:HOH954 3.9 43.1 1.0
OE2 D:GLU592 3.9 34.2 1.0
OG1 D:THR633 4.2 33.5 1.0
NE2 D:HIS595 4.2 38.4 1.0
CD2 D:HIS567 4.3 37.5 1.0
CD2 D:HIS563 4.4 32.2 1.0
OD2 D:ASP674 4.4 37.5 1.0
CD2 D:HIS595 4.4 37.7 1.0
NE2 D:HIS567 4.5 38.7 1.0
O D:HIS563 4.5 31.8 1.0
O D:THR633 4.5 38.8 1.0
CB D:ASP564 4.5 32.4 1.0
CB D:THR633 4.6 34.5 1.0
CD2 D:HIS525 4.7 39.6 1.0
O D:HOH968 4.7 35.5 1.0
NE2 D:HIS525 4.7 42.1 1.0
NE2 D:HIS563 4.8 31.9 1.0
CD D:GLU592 4.8 36.3 1.0
CA D:ASP564 4.9 32.7 1.0
CG D:GLU592 5.0 36.3 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 03:40:50 2024

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