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Magnesium in PDB 5seo: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione, PDB code: 5seo was solved by C.Joseph, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.277, 135.277, 235.581, 90, 90, 120
R / Rfree (%) 18.3 / 22.8

Other elements in 5seo:

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

Magnesium binding site 1 out of 4 in 5seo

Go back to Magnesium Binding Sites List in 5seo
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione


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 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:28.4
occ:1.00
 OD1 A:ASP564 1.9 27.1 1.0
O A:HOH945 2.0 30.4 1.0
O A:HOH1002 2.0 26.1 1.0
O A:HOH927 2.1 26.3 1.0
O A:HOH966 2.1 27.7 1.0
O A:HOH916 2.2 29.9 1.0
CG A:ASP564 2.9 30.2 1.0
OD2 A:ASP564 3.3 32.2 1.0
ZN A:ZN801 3.8 34.2 1.0
OE2 A:GLU592 3.9 37.8 1.0
O A:HOH986 4.0 39.2 1.0
NE2 A:HIS595 4.1 29.9 1.0
CD2 A:HIS563 4.2 26.7 1.0
OG1 A:THR633 4.3 32.8 1.0
O A:HOH980 4.3 35.6 1.0
CB A:ASP564 4.3 27.0 1.0
O A:HIS563 4.3 31.5 1.0
CD2 A:HIS595 4.4 29.2 1.0
CD2 A:HIS567 4.4 37.8 1.0
OD2 A:ASP674 4.4 40.4 1.0
O A:THR633 4.5 32.4 1.0
NE2 A:HIS563 4.5 26.0 1.0
NE2 A:HIS567 4.6 34.2 1.0
CD2 A:HIS525 4.7 36.1 1.0
CB A:THR633 4.7 31.1 1.0
CA A:ASP564 4.7 27.6 1.0
NE2 A:HIS525 4.8 35.4 1.0
CD A:GLU592 4.8 39.3 1.0
CG A:GLU592 4.8 36.4 1.0

Magnesium binding site 2 out of 4 in 5seo

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione


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 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.4
occ:1.00
 O B:HOH924 1.9 23.9 1.0
OD1 B:ASP564 2.0 28.4 1.0
O B:HOH925 2.0 25.2 1.0
O B:HOH1000 2.0 26.2 1.0
O B:HOH951 2.1 25.5 1.0
O B:HOH908 2.1 23.3 1.0
CG B:ASP564 3.1 30.8 1.0
OD2 B:ASP564 3.5 29.6 1.0
O B:HOH1024 3.8 53.6 1.0
ZN B:ZN801 3.8 33.8 1.0
OE2 B:GLU592 4.0 34.9 1.0
O B:HOH995 4.0 40.7 1.0
NE2 B:HIS595 4.0 31.5 1.0
O B:HIS563 4.2 29.8 1.0
CD2 B:HIS563 4.2 28.1 1.0
OG1 B:THR633 4.2 31.5 1.0
CD2 B:HIS595 4.3 34.0 1.0
CD2 B:HIS567 4.3 29.5 1.0
O B:HOH969 4.3 33.1 1.0
OD2 B:ASP674 4.3 32.4 1.0
CB B:ASP564 4.4 26.5 1.0
O B:THR633 4.4 31.0 1.0
NE2 B:HIS567 4.5 28.7 1.0
NE2 B:HIS563 4.6 27.0 1.0
CD2 B:HIS525 4.6 32.5 1.0
NE2 B:HIS525 4.7 31.8 1.0
CA B:ASP564 4.7 28.6 1.0
CB B:THR633 4.7 32.3 1.0
CG B:GLU592 4.7 32.6 1.0
CD B:GLU592 4.8 33.1 1.0
C B:HIS563 5.0 27.7 1.0

Magnesium binding site 3 out of 4 in 5seo

Go back to Magnesium Binding Sites List in 5seo
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione


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 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.9
occ:1.00
 O C:HOH930 2.0 32.8 1.0
O C:HOH991 2.0 28.1 1.0
O C:HOH943 2.1 28.9 1.0
O C:HOH931 2.1 32.8 1.0
OD1 C:ASP564 2.1 27.8 1.0
O C:HOH921 2.2 28.0 1.0
CG C:ASP564 3.1 31.1 1.0
OD2 C:ASP564 3.4 31.1 1.0
ZN C:ZN801 3.8 36.0 1.0
O C:HOH964 3.9 37.0 1.0
NE2 C:HIS595 4.0 30.3 1.0
OE2 C:GLU592 4.1 39.3 1.0
O C:HOH957 4.1 37.9 1.0
CD2 C:HIS567 4.2 33.9 1.0
CD2 C:HIS563 4.3 27.4 1.0
NE2 C:HIS567 4.4 30.8 1.0
OG1 C:THR633 4.4 36.0 1.0
CD2 C:HIS595 4.4 30.6 1.0
OD2 C:ASP674 4.4 36.5 1.0
O C:HIS563 4.4 29.5 1.0
O C:THR633 4.4 34.1 1.0
CB C:ASP564 4.4 28.4 1.0
CD2 C:HIS525 4.6 35.7 1.0
NE2 C:HIS525 4.7 35.9 1.0
NE2 C:HIS563 4.7 29.3 1.0
CB C:THR633 4.8 33.2 1.0
CA C:ASP564 4.8 29.2 1.0
CG C:GLU592 4.9 34.1 1.0
CD C:GLU592 4.9 37.4 1.0

Magnesium binding site 4 out of 4 in 5seo

Go back to Magnesium Binding Sites List in 5seo
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione


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 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:41.4
occ:1.00
 O D:HOH936 2.1 34.3 1.0
O D:HOH956 2.1 38.0 1.0
O D:HOH911 2.1 33.8 1.0
O D:HOH921 2.1 39.4 1.0
OD1 D:ASP564 2.2 39.2 1.0
O D:HOH922 2.2 40.3 1.0
CG D:ASP564 3.3 38.1 1.0
OD2 D:ASP564 3.6 43.2 1.0
O D:HOH946 3.7 46.3 1.0
O D:HOH947 3.9 44.8 1.0
ZN D:ZN801 3.9 44.9 1.0
OE2 D:GLU592 4.0 44.0 1.0
NE2 D:HIS595 4.1 43.8 1.0
CD2 D:HIS595 4.2 41.5 1.0
OG1 D:THR633 4.3 39.6 1.0
CD2 D:HIS567 4.3 50.9 1.0
OD2 D:ASP674 4.4 43.0 1.0
CD2 D:HIS563 4.4 39.8 1.0
O D:HIS563 4.4 34.7 1.0
O D:THR633 4.5 45.0 1.0
CB D:ASP564 4.6 39.0 1.0
NE2 D:HIS567 4.6 45.9 1.0
CB D:THR633 4.7 38.7 1.0
CD2 D:HIS525 4.7 46.1 1.0
O D:HOH954 4.8 47.5 1.0
CG D:GLU592 4.8 48.1 1.0
CD D:GLU592 4.8 44.1 1.0
NE2 D:HIS563 4.8 36.9 1.0
NE2 D:HIS525 4.8 53.0 1.0
CA D:ASP564 4.9 37.6 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Sep 30 03:25:26 2024

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