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Magnesium in PDB 5sec: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline, PDB code: 5sec 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) 43.80 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.753, 135.753, 235.97, 90, 90, 120
R / Rfree (%) 18.1 / 22.5

Other elements in 5sec:

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

Magnesium binding site 1 out of 4 in 5sec

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.7
occ:1.00
 O A:HOH984 1.9 29.2 1.0
OD1 A:ASP564 2.0 29.4 1.0
O A:HOH912 2.1 25.1 1.0
O A:HOH954 2.1 28.2 1.0
O A:HOH958 2.1 29.4 1.0
O A:HOH916 2.1 28.2 1.0
CG A:ASP564 3.0 31.2 1.0
OD2 A:ASP564 3.4 32.8 1.0
ZN A:ZN801 3.8 35.1 1.0
O A:HOH965 3.9 35.2 1.0
OE2 A:GLU592 4.0 38.9 1.0
NE2 A:HIS595 4.1 29.0 1.0
OG1 A:THR633 4.3 30.6 1.0
O A:HOH964 4.3 34.8 1.0
O A:HIS563 4.3 28.9 1.0
CD2 A:HIS563 4.3 27.1 1.0
CD2 A:HIS567 4.3 32.0 1.0
CB A:ASP564 4.4 29.2 1.0
CD2 A:HIS595 4.4 30.4 1.0
O A:THR633 4.5 33.6 1.0
OD2 A:ASP674 4.6 34.7 1.0
NE2 A:HIS567 4.6 29.6 1.0
CD2 A:HIS525 4.6 33.4 1.0
NE2 A:HIS525 4.6 32.2 1.0
NE2 A:HIS563 4.7 26.3 1.0
CB A:THR633 4.7 29.5 1.0
CA A:ASP564 4.8 28.7 1.0
CD A:GLU592 4.9 32.5 1.0
CG A:GLU592 4.9 32.6 1.0

Magnesium binding site 2 out of 4 in 5sec

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:27.5
occ:1.00
 O B:HOH938 1.9 23.0 1.0
O B:HOH940 2.0 27.2 1.0
O B:HOH910 2.0 25.2 1.0
OD1 B:ASP564 2.1 29.1 1.0
O B:HOH986 2.1 26.3 1.0
O B:HOH963 2.1 24.9 1.0
CG B:ASP564 3.1 30.5 1.0
OD2 B:ASP564 3.4 28.1 1.0
O B:HOH998 3.7 52.9 1.0
ZN B:ZN801 3.7 32.6 1.0
OE2 B:GLU592 3.9 30.3 1.0
O B:HOH958 3.9 37.0 1.0
NE2 B:HIS595 4.1 26.2 1.0
OG1 B:THR633 4.2 27.0 1.0
CD2 B:HIS563 4.2 26.5 1.0
O B:HIS563 4.3 30.1 1.0
CD2 B:HIS567 4.3 30.4 1.0
CD2 B:HIS595 4.3 27.5 1.0
OD2 B:ASP674 4.3 31.9 1.0
O B:HOH947 4.3 31.4 1.0
NE2 B:HIS567 4.4 27.9 1.0
CB B:ASP564 4.5 27.6 1.0
NE2 B:HIS563 4.6 23.9 1.0
CD2 B:HIS525 4.6 29.8 1.0
O B:THR633 4.6 27.2 1.0
NE2 B:HIS525 4.6 34.1 1.0
CB B:THR633 4.6 28.9 1.0
CA B:ASP564 4.7 27.6 1.0
CG B:GLU592 4.8 29.2 1.0
CD B:GLU592 4.8 29.7 1.0

Magnesium binding site 3 out of 4 in 5sec

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


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.1
occ:1.00
 OD1 C:ASP564 1.9 28.1 1.0
O C:HOH973 2.0 30.1 1.0
O C:HOH925 2.0 29.3 1.0
O C:HOH935 2.0 27.2 1.0
O C:HOH991 2.1 32.0 1.0
O C:HOH917 2.2 25.9 1.0
CG C:ASP564 3.0 30.3 1.0
OD2 C:ASP564 3.4 30.2 1.0
ZN C:ZN801 3.8 34.4 1.0
O C:HOH1011 3.9 42.7 1.0
OE2 C:GLU592 3.9 32.2 1.0
O C:HOH978 4.0 38.4 1.0
NE2 C:HIS595 4.1 29.5 1.0
CD2 C:HIS567 4.2 30.4 1.0
CD2 C:HIS563 4.2 26.2 1.0
OG1 C:THR633 4.2 30.4 1.0
O C:HIS563 4.3 28.9 1.0
O C:HOH967 4.3 29.6 1.0
CB C:ASP564 4.3 27.4 1.0
CD2 C:HIS595 4.4 24.9 1.0
OD2 C:ASP674 4.4 36.1 1.0
NE2 C:HIS567 4.5 28.8 1.0
O C:THR633 4.5 31.9 1.0
CD2 C:HIS525 4.6 29.0 1.0
NE2 C:HIS563 4.7 28.1 1.0
NE2 C:HIS525 4.7 34.5 1.0
CB C:THR633 4.7 32.9 1.0
CA C:ASP564 4.8 30.3 1.0
CD C:GLU592 4.8 33.0 1.0
CG C:GLU592 4.8 31.0 1.0

Magnesium binding site 4 out of 4 in 5sec

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline


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- (1,4-Diphenylimidazol-2-Yl)Ethyl]-3-Methylquinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.4
occ:1.00
 O D:HOH944 2.0 38.4 1.0
O D:HOH929 2.0 30.3 1.0
O D:HOH910 2.1 34.4 1.0
O D:HOH902 2.1 37.5 1.0
OD1 D:ASP564 2.1 35.7 1.0
O D:HOH935 2.1 32.1 1.0
CG D:ASP564 3.1 37.5 1.0
OD2 D:ASP564 3.5 43.5 1.0
ZN D:ZN801 3.7 42.2 1.0
O D:HOH926 3.9 43.1 1.0
O D:HOH947 4.0 41.3 1.0
NE2 D:HIS595 4.0 42.3 1.0
OE2 D:GLU592 4.0 41.0 1.0
OG1 D:THR633 4.1 35.9 1.0
CD2 D:HIS563 4.3 32.0 1.0
CD2 D:HIS595 4.3 42.1 1.0
O D:HIS563 4.3 39.9 1.0
CD2 D:HIS567 4.4 42.7 1.0
O D:THR633 4.4 41.9 1.0
OD2 D:ASP674 4.4 45.3 1.0
CB D:ASP564 4.5 37.1 1.0
CD2 D:HIS525 4.5 38.4 1.0
NE2 D:HIS525 4.6 46.6 1.0
NE2 D:HIS567 4.7 42.3 1.0
CB D:THR633 4.7 39.0 1.0
NE2 D:HIS563 4.8 29.8 1.0
CA D:ASP564 4.8 37.4 1.0
CG D:GLU592 4.8 45.6 1.0
CD D:GLU592 4.9 44.6 1.0
O D:HOH953 4.9 40.4 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 03:20:28 2024

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