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Magnesium in PDB 5sg3: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- [(E)-(4-Bromo-3,5-Dimethoxyphenyl)Methylideneamino]-2-Ethoxy-2-(4- Morpholin-4-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- Morpholin-4-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- Morpholin-4-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- Morpholin-4-Ylphenyl)Acetamide, PDB code: 5sg3 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) 43.68 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.445, 135.445, 235.303, 90, 90, 120
R / Rfree (%) 18.2 / 22.8

Other elements in 5sg3:

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

Zinc (Zn) 4 atoms
Bromine (Br) 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- Morpholin-4-Ylphenyl)Acetamide (pdb code 5sg3). 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- Morpholin-4-Ylphenyl)Acetamide, PDB code: 5sg3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sg3

Go back to Magnesium Binding Sites List in 5sg3
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- Morpholin-4-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- Morpholin-4-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.4
occ:1.00
 O A:HOH1023 2.0 19.0 1.0
O A:HOH932 2.0 18.9 1.0
O A:HOH967 2.0 23.8 1.0
O A:HOH987 2.1 19.5 1.0
OD1 A:ASP564 2.1 22.4 1.0
O A:HOH929 2.1 21.9 1.0
CG A:ASP564 3.1 25.4 1.0
OD2 A:ASP564 3.5 25.6 1.0
ZN A:ZN801 3.8 27.4 1.0
O A:HOH990 3.9 31.6 1.0
OE2 A:GLU592 4.1 26.5 1.0
OG1 A:THR633 4.2 24.1 1.0
NE2 A:HIS595 4.2 28.3 1.0
CD2 A:HIS567 4.3 25.3 1.0
CD2 A:HIS563 4.4 23.7 1.0
O A:THR633 4.4 24.2 1.0
O A:HOH956 4.4 37.8 1.0
CD2 A:HIS595 4.4 25.3 1.0
O A:HIS563 4.4 22.9 1.0
OD2 A:ASP674 4.4 30.1 1.0
CB A:ASP564 4.5 21.7 1.0
NE2 A:HIS567 4.5 26.5 1.0
CB A:THR633 4.7 24.1 1.0
NE2 A:HIS525 4.7 26.4 1.0
NE2 A:HIS563 4.7 25.2 1.0
CD2 A:HIS525 4.7 27.7 1.0
CA A:ASP564 4.8 22.3 1.0
CG A:GLU592 4.9 24.0 1.0
CD A:GLU592 4.9 25.8 1.0

Magnesium binding site 2 out of 4 in 5sg3

Go back to Magnesium Binding Sites List in 5sg3
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- Morpholin-4-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- Morpholin-4-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:21.3
occ:1.00
 O B:HOH975 2.0 17.4 1.0
O B:HOH943 2.0 19.3 1.0
O B:HOH931 2.0 22.2 1.0
O B:HOH997 2.1 17.9 1.0
OD1 B:ASP564 2.1 22.0 1.0
O B:HOH1014 2.1 18.6 1.0
CG B:ASP564 3.1 21.1 1.0
OD2 B:ASP564 3.5 23.0 1.0
ZN B:ZN801 3.8 26.9 1.0
NE2 B:HIS595 4.1 22.1 1.0
OE2 B:GLU592 4.1 30.5 1.0
O B:HOH995 4.1 32.6 1.0
OG1 B:THR633 4.1 21.5 1.0
CD2 B:HIS567 4.3 18.4 1.0
CD2 B:HIS563 4.3 22.3 1.0
CD2 B:HIS595 4.4 20.1 1.0
NE2 B:HIS567 4.4 21.5 1.0
O B:HIS563 4.4 21.2 1.0
OD2 B:ASP674 4.4 23.5 1.0
CB B:ASP564 4.5 20.6 1.0
O B:HOH994 4.5 33.9 1.0
O B:THR633 4.5 22.1 1.0
CD2 B:HIS525 4.6 26.6 1.0
NE2 B:HIS563 4.7 19.9 1.0
CB B:THR633 4.7 25.5 1.0
NE2 B:HIS525 4.7 26.7 1.0
CG B:GLU592 4.7 27.0 1.0
CA B:ASP564 4.8 22.3 1.0
CD B:GLU592 4.8 26.3 1.0

Magnesium binding site 3 out of 4 in 5sg3

Go back to Magnesium Binding Sites List in 5sg3
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- Morpholin-4-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- Morpholin-4-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.3
occ:1.00
 O C:HOH1038 2.0 22.7 1.0
O C:HOH992 2.0 23.1 1.0
O C:HOH958 2.0 19.8 1.0
OD1 C:ASP564 2.0 19.9 1.0
O C:HOH943 2.0 24.5 1.0
O C:HOH962 2.1 22.2 1.0
CG C:ASP564 3.1 25.3 1.0
OD2 C:ASP564 3.4 23.2 1.0
ZN C:ZN801 3.8 30.1 1.0
O C:HOH999 4.0 35.3 1.0
OE2 C:GLU592 4.1 29.4 1.0
NE2 C:HIS595 4.1 25.4 1.0
CD2 C:HIS567 4.2 29.2 1.0
CD2 C:HIS563 4.2 22.2 1.0
OG1 C:THR633 4.3 25.1 1.0
O C:HIS563 4.3 24.4 1.0
CD2 C:HIS595 4.4 23.3 1.0
NE2 C:HIS567 4.4 26.5 1.0
OD2 C:ASP674 4.4 30.7 1.0
CB C:ASP564 4.4 20.6 1.0
O C:THR633 4.5 25.0 1.0
NE2 C:HIS563 4.6 25.4 1.0
O C:HOH994 4.6 39.9 1.0
CB C:THR633 4.7 22.9 1.0
CA C:ASP564 4.7 21.4 1.0
CD2 C:HIS525 4.7 28.1 1.0
NE2 C:HIS525 4.8 32.6 1.0
CG C:GLU592 4.8 26.1 1.0
CD C:GLU592 4.9 25.9 1.0

Magnesium binding site 4 out of 4 in 5sg3

Go back to Magnesium Binding Sites List in 5sg3
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- Morpholin-4-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- Morpholin-4-Ylphenyl)Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:27.6
occ:1.00
 O D:HOH997 1.9 27.4 1.0
O D:HOH944 2.0 23.8 1.0
O D:HOH935 2.1 26.6 1.0
O D:HOH931 2.1 28.3 1.0
O D:HOH983 2.1 23.2 1.0
OD1 D:ASP564 2.2 25.5 1.0
CG D:ASP564 3.1 27.7 1.0
OD2 D:ASP564 3.5 29.7 1.0
ZN D:ZN801 3.8 33.0 1.0
O D:HOH986 3.8 38.3 1.0
OE2 D:GLU592 4.1 34.3 1.0
OG1 D:THR633 4.2 28.6 1.0
NE2 D:HIS595 4.2 31.8 1.0
O D:HOH978 4.2 34.7 1.0
CD2 D:HIS563 4.3 27.9 1.0
CD2 D:HIS567 4.4 34.8 1.0
OD2 D:ASP674 4.4 31.1 1.0
O D:HIS563 4.4 27.1 1.0
CD2 D:HIS595 4.4 27.7 1.0
CB D:ASP564 4.5 27.6 1.0
O D:THR633 4.5 36.2 1.0
NE2 D:HIS567 4.6 31.5 1.0
CB D:THR633 4.7 31.9 1.0
CD2 D:HIS525 4.7 37.0 1.0
NE2 D:HIS563 4.7 23.6 1.0
CA D:ASP564 4.8 26.6 1.0
NE2 D:HIS525 4.8 36.0 1.0
CG D:GLU592 4.8 36.0 1.0
CD D:GLU592 4.9 33.1 1.0
O D:HOH1000 5.0 33.4 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: Tue Aug 12 19:35:16 2025

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