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Magnesium in PDB 5sii: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine, PDB code: 5sii was solved by C.Joseph, J.Benz, A.Flohr, P.Zeller, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.71 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.531, 135.531, 235.479, 90, 90, 120
R / Rfree (%) 17.5 / 22.5

Other elements in 5sii:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine 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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine (pdb code 5sii). 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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine, PDB code: 5sii:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sii

Go back to Magnesium Binding Sites List in 5sii
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.6
occ:1.00
 O A:HOH971 1.9 30.7 1.0
O A:HOH987 1.9 28.9 1.0
OD1 A:ASP564 1.9 34.5 1.0
O A:HOH908 2.1 27.6 1.0
O A:HOH946 2.1 33.9 1.0
O A:HOH938 2.2 30.0 1.0
CG A:ASP564 2.9 31.5 1.0
OD2 A:ASP564 3.3 31.0 1.0
ZN A:ZN801 3.7 36.6 1.0
O A:HOH967 3.9 39.2 1.0
NE2 A:HIS595 4.1 30.7 1.0
OE2 A:GLU592 4.2 39.4 1.0
O A:HOH962 4.2 45.9 1.0
CD2 A:HIS563 4.3 28.3 1.0
CD2 A:HIS567 4.3 40.3 1.0
CB A:ASP564 4.3 29.9 1.0
OG1 A:THR633 4.3 36.5 1.0
O A:HIS563 4.4 34.0 1.0
CD2 A:HIS595 4.4 31.8 1.0
NE2 A:HIS567 4.5 40.1 1.0
O A:THR633 4.6 35.6 1.0
NE2 A:HIS563 4.6 31.5 1.0
OD2 A:ASP674 4.6 40.5 1.0
CD2 A:HIS525 4.6 37.6 1.0
NE2 A:HIS525 4.7 38.7 1.0
CA A:ASP564 4.8 32.8 1.0
CB A:THR633 4.8 31.6 1.0
CG A:GLU592 4.9 33.8 1.0
CD A:GLU592 5.0 41.2 1.0

Magnesium binding site 2 out of 4 in 5sii

Go back to Magnesium Binding Sites List in 5sii
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.9
occ:1.00
 O B:HOH957 1.9 25.2 1.0
O B:HOH943 1.9 25.0 1.0
O B:HOH996 2.0 26.9 1.0
OD1 B:ASP564 2.0 29.9 1.0
O B:HOH930 2.0 23.0 1.0
O B:HOH959 2.1 27.0 1.0
CG B:ASP564 3.0 28.8 1.0
OD2 B:ASP564 3.4 30.5 1.0
ZN B:ZN801 3.7 33.9 1.0
O B:HOH980 4.1 38.5 1.0
CD2 B:HIS563 4.1 31.9 1.0
OE2 B:GLU592 4.1 31.3 1.0
NE2 B:HIS595 4.1 31.4 1.0
OG1 B:THR633 4.2 31.1 1.0
O B:HIS563 4.3 31.9 1.0
CD2 B:HIS567 4.3 34.3 1.0
O B:HOH939 4.3 41.3 1.0
CB B:ASP564 4.4 27.9 1.0
CD2 B:HIS595 4.4 37.3 1.0
OD2 B:ASP674 4.4 39.2 1.0
NE2 B:HIS563 4.5 28.4 1.0
NE2 B:HIS567 4.5 32.1 1.0
O B:THR633 4.6 34.3 1.0
CA B:ASP564 4.6 29.2 1.0
CB B:THR633 4.7 33.6 1.0
CD2 B:HIS525 4.7 34.2 1.0
NE2 B:HIS525 4.7 36.6 1.0
CG B:GLU592 4.8 35.0 1.0
CD B:GLU592 4.9 32.1 1.0

Magnesium binding site 3 out of 4 in 5sii

Go back to Magnesium Binding Sites List in 5sii
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:28.3
occ:1.00
 O C:HOH943 2.0 25.8 1.0
O C:HOH914 2.0 28.9 1.0
O C:HOH948 2.0 24.3 1.0
O C:HOH995 2.0 31.3 1.0
OD1 C:ASP564 2.1 29.3 1.0
O C:HOH912 2.1 25.9 1.0
CG C:ASP564 3.1 30.4 1.0
OD2 C:ASP564 3.4 30.5 1.0
ZN C:ZN801 3.8 36.9 1.0
O C:HOH965 3.9 42.2 1.0
OE2 C:GLU592 4.1 36.7 1.0
NE2 C:HIS595 4.2 36.4 1.0
CD2 C:HIS563 4.2 31.5 1.0
O C:HOH954 4.2 42.7 1.0
CD2 C:HIS567 4.3 34.9 1.0
OG1 C:THR633 4.3 33.5 1.0
OD2 C:ASP674 4.3 38.7 1.0
NE2 C:HIS567 4.4 34.3 1.0
O C:HIS563 4.4 30.4 1.0
O C:THR633 4.4 35.6 1.0
CD2 C:HIS595 4.5 33.6 1.0
CB C:ASP564 4.5 28.5 1.0
NE2 C:HIS563 4.6 32.1 1.0
NE2 C:HIS525 4.6 36.4 1.0
CB C:THR633 4.7 31.2 1.0
CD2 C:HIS525 4.7 36.3 1.0
CG C:GLU592 4.9 34.7 1.0
CD C:GLU592 4.9 40.5 1.0
CA C:ASP564 4.9 30.0 1.0

Magnesium binding site 4 out of 4 in 5sii

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.0
occ:1.00
 O D:HOH945 2.0 28.9 1.0
O D:HOH957 2.0 40.0 1.0
O D:HOH915 2.0 34.8 1.0
O D:HOH947 2.1 39.5 1.0
O D:HOH913 2.1 30.2 1.0
OD1 D:ASP564 2.1 38.7 1.0
CG D:ASP564 3.1 37.9 1.0
OD2 D:ASP564 3.5 36.0 1.0
ZN D:ZN801 3.8 42.3 1.0
O D:HOH941 3.9 43.1 1.0
OE2 D:GLU592 4.0 41.9 1.0
NE2 D:HIS595 4.1 44.7 1.0
CD2 D:HIS567 4.2 44.8 1.0
OG1 D:THR633 4.2 39.4 1.0
O D:HOH952 4.3 49.7 1.0
NE2 D:HIS567 4.4 41.7 1.0
OD2 D:ASP674 4.4 49.9 1.0
CD2 D:HIS563 4.4 33.2 1.0
CD2 D:HIS595 4.4 42.2 1.0
O D:THR633 4.4 43.9 1.0
O D:HIS563 4.5 36.5 1.0
CB D:ASP564 4.5 33.8 1.0
NE2 D:HIS525 4.6 47.5 1.0
CD2 D:HIS525 4.6 42.5 1.0
NE2 D:HIS563 4.8 31.2 1.0
CB D:THR633 4.8 39.8 1.0
CD D:GLU592 4.9 42.3 1.0
CA D:ASP564 4.9 36.6 1.0
CG D:GLU592 4.9 47.4 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 19:58:03 2025

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