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Magnesium in PDB 5sgl: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide, PDB code: 5sgl 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) 43.72 / 2.28
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.574, 135.574, 235.517, 90, 90, 120
R / Rfree (%) 18.1 / 23

Other elements in 5sgl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide also contains other interesting chemical elements:

Bromine (Br) 4 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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide (pdb code 5sgl). 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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide, PDB code: 5sgl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgl

Go back to Magnesium Binding Sites List in 5sgl
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.1
occ:1.00
 O A:HOH990 1.9 30.8 1.0
O A:HOH921 2.0 28.6 1.0
O A:HOH964 2.1 26.6 1.0
O A:HOH943 2.1 26.3 1.0
O A:HOH913 2.2 41.7 1.0
OD1 A:ASP564 2.2 32.6 1.0
CG A:ASP564 3.1 34.0 1.0
OD2 A:ASP564 3.3 37.0 1.0
ZN A:ZN801 3.9 39.5 1.0
O A:HOH942 3.9 43.1 1.0
O A:HOH970 3.9 42.1 1.0
NE2 A:HIS595 4.1 32.3 1.0
CD2 A:HIS567 4.2 40.3 1.0
OE2 A:GLU592 4.2 41.5 1.0
OG1 A:THR633 4.4 35.1 1.0
NE2 A:HIS567 4.4 39.8 1.0
CD2 A:HIS595 4.4 30.1 1.0
CD2 A:HIS563 4.4 33.3 1.0
O A:HIS563 4.4 35.2 1.0
CB A:ASP564 4.5 32.7 1.0
O A:THR633 4.5 34.8 1.0
OD2 A:ASP674 4.6 44.5 1.0
CD2 A:HIS525 4.6 36.5 1.0
NE2 A:HIS525 4.7 36.1 1.0
CB A:THR633 4.8 33.0 1.0
NE2 A:HIS563 4.8 32.0 1.0
CG A:GLU592 4.9 34.6 1.0
CD A:GLU592 4.9 37.7 1.0
CA A:ASP564 4.9 32.9 1.0

Magnesium binding site 2 out of 4 in 5sgl

Go back to Magnesium Binding Sites List in 5sgl
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:27.3
occ:1.00
 O B:HOH944 1.9 28.8 1.0
O B:HOH960 1.9 25.1 1.0
O B:HOH958 2.0 24.0 1.0
O B:HOH976 2.0 29.7 1.0
O B:HOH906 2.1 20.6 1.0
OD1 B:ASP564 2.1 28.1 1.0
CG B:ASP564 3.1 30.9 1.0
OD2 B:ASP564 3.5 29.5 1.0
ZN B:ZN801 3.8 34.8 1.0
O B:HOH970 3.9 43.8 1.0
OE2 B:GLU592 4.1 30.1 1.0
NE2 B:HIS595 4.1 29.0 1.0
CD2 B:HIS563 4.2 30.1 1.0
OG1 B:THR633 4.3 28.5 1.0
O B:HOH963 4.3 37.2 1.0
CD2 B:HIS567 4.3 30.2 1.0
CD2 B:HIS595 4.4 32.2 1.0
O B:HIS563 4.4 33.5 1.0
OD2 B:ASP674 4.4 34.6 1.0
NE2 B:HIS567 4.4 34.0 1.0
CB B:ASP564 4.5 29.9 1.0
NE2 B:HIS563 4.6 28.6 1.0
O B:THR633 4.6 30.0 1.0
CD2 B:HIS525 4.6 31.6 1.0
NE2 B:HIS525 4.7 32.6 1.0
CB B:THR633 4.7 31.1 1.0
CA B:ASP564 4.8 31.5 1.0
CG B:GLU592 4.8 34.2 1.0
CD B:GLU592 4.9 33.8 1.0

Magnesium binding site 3 out of 4 in 5sgl

Go back to Magnesium Binding Sites List in 5sgl
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.3
occ:1.00
 O C:HOH964 1.9 28.0 1.0
O C:HOH935 2.0 24.9 1.0
O C:HOH941 2.1 32.2 1.0
OD1 C:ASP564 2.1 31.9 1.0
O C:HOH928 2.1 24.7 1.0
O C:HOH984 2.2 26.6 1.0
CG C:ASP564 3.1 31.2 1.0
OD2 C:ASP564 3.5 31.6 1.0
ZN C:ZN801 3.8 38.1 1.0
OE2 C:GLU592 4.0 36.3 1.0
O C:HOH970 4.1 42.7 1.0
NE2 C:HIS595 4.2 35.7 1.0
CD2 C:HIS567 4.2 32.8 1.0
NE2 C:HIS567 4.3 34.2 1.0
CD2 C:HIS563 4.3 30.8 1.0
O C:HOH953 4.3 44.4 1.0
OD2 C:ASP674 4.4 38.9 1.0
OG1 C:THR633 4.4 32.7 1.0
O C:HIS563 4.4 33.2 1.0
CD2 C:HIS595 4.4 35.7 1.0
CB C:ASP564 4.5 29.9 1.0
O C:THR633 4.5 35.1 1.0
CB C:THR633 4.7 33.4 1.0
CD2 C:HIS525 4.7 39.8 1.0
NE2 C:HIS563 4.8 34.7 1.0
CA C:ASP564 4.8 30.9 1.0
NE2 C:HIS525 4.8 43.9 1.0
CD C:GLU592 4.9 38.2 1.0
CG C:GLU592 5.0 35.8 1.0

Magnesium binding site 4 out of 4 in 5sgl

Go back to Magnesium Binding Sites List in 5sgl
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide


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 N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Pyrazol-1-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:43.4
occ:1.00
 O D:HOH935 2.0 55.5 1.0
O D:HOH938 2.0 39.5 1.0
O D:HOH930 2.1 33.7 1.0
O D:HOH925 2.1 29.9 1.0
OD1 D:ASP564 2.2 41.5 1.0
O D:HOH909 2.2 33.4 1.0
CG D:ASP564 3.2 40.3 1.0
OD2 D:ASP564 3.5 42.9 1.0
O D:HOH944 3.8 47.7 1.0
NE2 D:HIS595 3.9 47.6 1.0
ZN D:ZN801 3.9 45.7 1.0
CD2 D:HIS567 4.0 51.9 1.0
O D:HOH928 4.0 40.2 1.0
OE2 D:GLU592 4.2 41.2 1.0
CD2 D:HIS595 4.2 45.3 1.0
NE2 D:HIS567 4.2 51.9 1.0
OG1 D:THR633 4.3 36.1 1.0
CD2 D:HIS563 4.4 39.0 1.0
O D:HIS563 4.4 39.2 1.0
CD2 D:HIS525 4.5 50.3 1.0
CB D:ASP564 4.5 39.2 1.0
OD2 D:ASP674 4.6 50.1 1.0
NE2 D:HIS525 4.6 49.1 1.0
O D:THR633 4.7 40.2 1.0
NE2 D:HIS563 4.8 37.8 1.0
CD D:GLU592 4.8 44.7 1.0
CG D:GLU592 4.8 43.3 1.0
CA D:ASP564 4.9 39.1 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 03:49:04 2024

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