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Magnesium in PDB 5seb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline, PDB code: 5seb was solved by C.Joseph, A.Flohr, 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) 43.67 / 2.28
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.375, 135.375, 235.267, 90, 90, 120
R / Rfree (%) 17.4 / 22.3

Other elements in 5seb:

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

Magnesium binding site 1 out of 4 in 5seb

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


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- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:36.4
occ:1.00
 O A:HOH977 1.9 35.9 1.0
OD1 A:ASP564 2.0 38.5 1.0
O A:HOH905 2.0 31.8 1.0
O A:HOH937 2.1 32.6 1.0
O A:HOH938 2.2 35.1 1.0
O A:HOH918 2.2 38.1 1.0
CG A:ASP564 2.9 37.9 1.0
OD2 A:ASP564 3.2 41.8 1.0
ZN A:ZN801 3.7 44.1 1.0
O A:HOH965 3.8 56.4 1.0
O A:HOH941 3.9 40.1 1.0
NE2 A:HIS595 4.1 35.8 1.0
O A:HOH932 4.1 44.7 1.0
OE2 A:GLU592 4.2 41.3 1.0
CD2 A:HIS567 4.3 38.1 1.0
CD2 A:HIS563 4.3 35.9 1.0
CB A:ASP564 4.3 35.5 1.0
O A:HIS563 4.3 41.0 1.0
OG1 A:THR633 4.3 40.7 1.0
CD2 A:HIS595 4.4 34.1 1.0
NE2 A:HIS525 4.4 43.1 1.0
CD2 A:HIS525 4.5 43.2 1.0
NE2 A:HIS567 4.5 40.1 1.0
O A:THR633 4.5 39.5 1.0
OD2 A:ASP674 4.6 41.5 1.0
NE2 A:HIS563 4.6 35.0 1.0
CB A:THR633 4.8 40.6 1.0
CA A:ASP564 4.8 38.9 1.0
CG A:GLU592 4.9 37.9 1.0

Magnesium binding site 2 out of 4 in 5seb

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


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- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.9
occ:1.00
 O B:HOH945 1.9 31.6 1.0
O B:HOH922 2.0 33.4 1.0
O B:HOH963 2.0 30.1 1.0
OD1 B:ASP564 2.1 36.9 1.0
O B:HOH908 2.1 31.0 1.0
O B:HOH931 2.1 31.1 1.0
CG B:ASP564 3.1 36.0 1.0
O B:HOH983 3.4 59.9 1.0
OD2 B:ASP564 3.4 40.5 1.0
ZN B:ZN801 3.7 42.3 1.0
O B:HOH923 3.9 44.5 1.0
NE2 B:HIS595 4.1 37.2 1.0
O B:HOH961 4.1 37.1 1.0
OE2 B:GLU592 4.1 34.6 1.0
CD2 B:HIS563 4.2 38.6 1.0
CD2 B:HIS567 4.2 35.9 1.0
NE2 B:HIS567 4.3 39.5 1.0
OG1 B:THR633 4.3 38.4 1.0
CD2 B:HIS595 4.4 41.3 1.0
OD2 B:ASP674 4.4 41.7 1.0
CB B:ASP564 4.4 35.0 1.0
O B:HIS563 4.4 37.8 1.0
CD2 B:HIS525 4.5 36.7 1.0
NE2 B:HIS563 4.6 36.5 1.0
NE2 B:HIS525 4.6 35.4 1.0
O B:THR633 4.6 34.9 1.0
CB B:THR633 4.7 37.0 1.0
CA B:ASP564 4.8 36.7 1.0
CG B:GLU592 4.9 36.9 1.0
CD B:GLU592 4.9 37.5 1.0

Magnesium binding site 3 out of 4 in 5seb

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


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- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:36.5
occ:1.00
 O C:HOH930 1.9 41.4 1.0
O C:HOH969 2.0 38.2 1.0
O C:HOH940 2.0 29.5 1.0
OD1 C:ASP564 2.1 39.4 1.0
O C:HOH976 2.2 37.0 1.0
O C:HOH932 2.2 30.9 1.0
CG C:ASP564 3.1 36.0 1.0
OD2 C:ASP564 3.5 39.0 1.0
ZN C:ZN801 3.8 42.0 1.0
O C:HOH981 3.8 43.1 1.0
OE2 C:GLU592 3.9 38.2 1.0
NE2 C:HIS595 4.0 42.3 1.0
O C:HOH964 4.1 44.2 1.0
O C:HOH953 4.1 38.9 1.0
CD2 C:HIS567 4.2 37.0 1.0
CD2 C:HIS563 4.3 33.3 1.0
CD2 C:HIS595 4.3 39.5 1.0
O C:HIS563 4.3 36.8 1.0
OG1 C:THR633 4.3 36.3 1.0
NE2 C:HIS567 4.4 40.3 1.0
CB C:ASP564 4.4 35.7 1.0
OD2 C:ASP674 4.5 36.6 1.0
O C:THR633 4.6 37.6 1.0
CB C:THR633 4.7 38.7 1.0
NE2 C:HIS525 4.7 39.9 1.0
CD2 C:HIS525 4.7 38.3 1.0
NE2 C:HIS563 4.7 36.1 1.0
CA C:ASP564 4.8 37.5 1.0
CD C:GLU592 4.8 37.8 1.0
CG C:GLU592 4.8 38.6 1.0

Magnesium binding site 4 out of 4 in 5seb

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


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- Methyl-3-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl) Ethyl]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:53.2
occ:1.00
 O D:HOH926 2.0 44.9 1.0
OD1 D:ASP564 2.0 52.9 1.0
O D:HOH920 2.1 40.3 1.0
O D:HOH902 2.1 52.1 1.0
O D:HOH927 2.1 50.6 1.0
O D:HOH903 2.2 47.3 1.0
CG D:ASP564 3.0 50.4 1.0
OD2 D:ASP564 3.3 60.5 1.0
ZN D:ZN801 3.8 55.9 1.0
O D:HOH928 3.8 51.4 1.0
O D:HOH909 3.9 47.2 1.0
NE2 D:HIS595 4.0 55.5 1.0
OE2 D:GLU592 4.1 51.9 1.0
CD2 D:HIS563 4.2 45.4 1.0
CD2 D:HIS567 4.3 50.0 1.0
CD2 D:HIS595 4.3 57.0 1.0
O D:HIS563 4.3 51.2 1.0
OG1 D:THR633 4.3 49.4 1.0
CB D:ASP564 4.4 48.3 1.0
OD2 D:ASP674 4.6 54.5 1.0
CD2 D:HIS525 4.6 59.1 1.0
O D:THR633 4.6 52.5 1.0
NE2 D:HIS563 4.6 42.5 1.0
NE2 D:HIS567 4.6 50.8 1.0
NE2 D:HIS525 4.7 58.6 1.0
CB D:THR633 4.7 55.3 1.0
CA D:ASP564 4.7 47.1 1.0
CG D:GLU592 4.9 54.6 1.0
CD D:GLU592 4.9 50.2 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 03:20:17 2024

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