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Magnesium in PDB 5se2: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline, PDB code: 5se2 was solved by C.Joseph, K.Groebke-Zbinden, 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) 43.72 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.003, 135.003, 235.705, 90, 90, 120
R / Rfree (%) 19.4 / 22.1

Other elements in 5se2:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline 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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline (pdb code 5se2). 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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline, PDB code: 5se2:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se2

Go back to Magnesium Binding Sites List in 5se2
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.9
occ:1.00
 O A:HOH959 1.9 34.3 1.0
O A:HOH933 1.9 31.3 1.0
OD1 A:ASP564 2.0 32.3 1.0
O A:HOH993 2.1 31.5 1.0
O A:HOH968 2.1 36.1 1.0
O A:HOH925 2.1 32.5 1.0
CG A:ASP564 3.0 32.3 1.0
OD2 A:ASP564 3.3 29.4 1.0
ZN A:ZN801 3.7 35.2 1.0
O A:HOH1020 3.8 51.6 1.0
O A:HOH981 3.9 50.6 1.0
NE2 A:HIS595 4.1 35.9 1.0
OE2 A:GLU592 4.1 42.5 1.0
CD2 A:HIS563 4.2 29.6 1.0
CD2 A:HIS567 4.3 39.9 1.0
O A:HOH966 4.3 41.5 1.0
CD2 A:HIS595 4.3 35.0 1.0
O A:HIS563 4.3 35.4 1.0
CB A:ASP564 4.3 31.6 1.0
OG1 A:THR633 4.4 38.6 1.0
O A:THR633 4.5 40.3 1.0
NE2 A:HIS563 4.5 30.4 1.0
OD2 A:ASP674 4.5 34.8 1.0
NE2 A:HIS567 4.6 35.6 1.0
NE2 A:HIS525 4.6 34.9 1.0
CD2 A:HIS525 4.6 37.9 1.0
CA A:ASP564 4.7 33.3 1.0
CB A:THR633 4.8 35.6 1.0
CD A:GLU592 4.9 39.2 1.0
CG A:GLU592 4.9 35.7 1.0

Magnesium binding site 2 out of 4 in 5se2

Go back to Magnesium Binding Sites List in 5se2
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.6
occ:1.00
 O B:HOH922 2.0 31.0 1.0
O B:HOH991 2.1 28.6 1.0
O B:HOH937 2.1 27.6 1.0
OD1 B:ASP564 2.1 30.8 1.0
O B:HOH952 2.1 29.8 1.0
O B:HOH965 2.1 32.7 1.0
CG B:ASP564 3.1 29.2 1.0
OD2 B:ASP564 3.5 26.4 1.0
OE2 B:GLU592 3.9 35.0 1.0
ZN B:ZN801 3.9 37.3 1.0
O B:HOH976 4.0 61.5 1.0
O B:HOH940 4.0 39.8 1.0
NE2 B:HIS595 4.1 33.4 1.0
CD2 B:HIS567 4.1 30.1 1.0
O B:HOH999 4.2 35.3 1.0
NE2 B:HIS567 4.2 27.9 1.0
CD2 B:HIS563 4.3 29.6 1.0
CD2 B:HIS595 4.3 33.9 1.0
OG1 B:THR633 4.3 31.9 1.0
O B:HIS563 4.4 36.7 1.0
CB B:ASP564 4.5 28.2 1.0
OD2 B:ASP674 4.5 34.2 1.0
O B:THR633 4.5 35.1 1.0
CD2 B:HIS525 4.6 31.4 1.0
NE2 B:HIS525 4.6 30.9 1.0
NE2 B:HIS563 4.6 29.5 1.0
CD B:GLU592 4.8 34.9 1.0
CB B:THR633 4.8 34.8 1.0
CA B:ASP564 4.9 30.9 1.0
CG B:GLU592 4.9 36.2 1.0

Magnesium binding site 3 out of 4 in 5se2

Go back to Magnesium Binding Sites List in 5se2
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:34.2
occ:1.00
 O C:HOH934 2.0 30.1 1.0
OD1 C:ASP564 2.0 32.0 1.0
O C:HOH933 2.1 36.1 1.0
O C:HOH950 2.1 30.4 1.0
O C:HOH1012 2.2 33.0 1.0
O C:HOH976 2.2 34.1 1.0
CG C:ASP564 3.1 31.7 1.0
OD2 C:ASP564 3.5 34.1 1.0
ZN C:ZN801 3.9 40.0 1.0
OE2 C:GLU592 4.0 40.1 1.0
NE2 C:HIS595 4.0 33.0 1.0
O C:HOH981 4.1 43.8 1.0
OG1 C:THR633 4.2 36.6 1.0
CD2 C:HIS563 4.2 31.0 1.0
CD2 C:HIS567 4.2 36.2 1.0
CD2 C:HIS595 4.3 31.1 1.0
O C:HIS563 4.3 34.0 1.0
O C:HOH1017 4.3 60.4 1.0
O C:THR633 4.4 37.4 1.0
CB C:ASP564 4.4 30.9 1.0
NE2 C:HIS567 4.5 36.6 1.0
OD2 C:ASP674 4.5 37.3 1.0
NE2 C:HIS563 4.5 33.4 1.0
O C:HOH992 4.6 38.7 1.0
CB C:THR633 4.7 35.2 1.0
CA C:ASP564 4.8 34.0 1.0
CG C:GLU592 4.8 38.1 1.0
CD2 C:HIS525 4.8 35.2 1.0
NE2 C:HIS525 4.8 34.8 1.0
CD C:GLU592 4.8 39.0 1.0

Magnesium binding site 4 out of 4 in 5se2

Go back to Magnesium Binding Sites List in 5se2
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline


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- (1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:42.5
occ:1.00
 O D:HOH920 2.0 44.1 1.0
O D:HOH941 2.1 45.3 1.0
O D:HOH917 2.1 37.3 1.0
O D:HOH956 2.2 41.6 1.0
O D:HOH902 2.2 43.5 1.0
OD1 D:ASP564 2.2 40.9 1.0
CG D:ASP564 3.2 42.5 1.0
OD2 D:ASP564 3.5 51.8 1.0
O D:HOH923 3.9 39.7 1.0
ZN D:ZN801 3.9 48.3 1.0
O D:HOH932 3.9 44.4 1.0
OE2 D:GLU592 4.0 46.0 1.0
NE2 D:HIS595 4.2 44.7 1.0
OG1 D:THR633 4.3 40.7 1.0
CD2 D:HIS567 4.3 44.4 1.0
O D:HIS563 4.3 38.4 1.0
CD2 D:HIS563 4.4 38.9 1.0
OD2 D:ASP674 4.4 43.4 1.0
NE2 D:HIS567 4.4 46.7 1.0
CD2 D:HIS595 4.5 45.8 1.0
O D:THR633 4.5 50.5 1.0
CB D:ASP564 4.5 42.6 1.0
CB D:THR633 4.6 45.3 1.0
CD2 D:HIS525 4.7 47.9 1.0
CG D:GLU592 4.7 48.5 1.0
NE2 D:HIS525 4.7 50.2 1.0
CD D:GLU592 4.8 48.5 1.0
NE2 D:HIS563 4.8 37.2 1.0
CA D:ASP564 4.9 41.6 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 03:17:23 2024

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