Atomistry » Magnesium » PDB 5ses-5sfv » 5sev
Atomistry »
  Magnesium »
    PDB 5ses-5sfv »
      5sev »

Magnesium in PDB 5sev: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine, PDB code: 5sev 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) 43.76 / 2.31
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.434, 135.434, 235.847, 90, 90, 120
R / Rfree (%) 17.9 / 23.1

Other elements in 5sev:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine (pdb code 5sev). 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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine, PDB code: 5sev:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sev

Go back to Magnesium Binding Sites List in 5sev
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.6
occ:1.00
 O A:HOH962 2.0 27.1 1.0
O A:HOH966 2.0 30.8 1.0
OD1 A:ASP564 2.0 36.4 1.0
O A:HOH947 2.0 32.0 1.0
O A:HOH991 2.0 26.0 1.0
O A:HOH915 2.1 33.2 1.0
CG A:ASP564 3.0 37.5 1.0
OD2 A:ASP564 3.3 37.7 1.0
ZN A:ZN801 3.8 40.1 1.0
O A:HOH954 4.0 38.9 1.0
OE2 A:GLU592 4.0 50.8 1.0
NE2 A:HIS595 4.0 41.9 1.0
O A:HOH961 4.2 44.4 1.0
CD2 A:HIS567 4.3 38.7 1.0
OG1 A:THR633 4.3 40.6 1.0
CD2 A:HIS595 4.3 36.4 1.0
CB A:ASP564 4.4 34.1 1.0
O A:HIS563 4.4 35.9 1.0
CD2 A:HIS563 4.4 31.2 1.0
O A:THR633 4.5 37.6 1.0
NE2 A:HIS567 4.5 39.9 1.0
OD2 A:ASP674 4.6 52.3 1.0
NE2 A:HIS525 4.7 39.5 1.0
NE2 A:HIS563 4.7 32.5 1.0
CD2 A:HIS525 4.7 43.2 1.0
CA A:ASP564 4.8 35.1 1.0
CB A:THR633 4.8 37.5 1.0
CG A:GLU592 4.8 42.4 1.0
CD A:GLU592 4.8 46.2 1.0

Magnesium binding site 2 out of 4 in 5sev

Go back to Magnesium Binding Sites List in 5sev
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:32.5
occ:1.00
 O B:HOH939 1.9 25.6 1.0
O B:HOH922 1.9 31.3 1.0
O B:HOH973 2.0 25.6 1.0
OD1 B:ASP564 2.0 31.9 1.0
O B:HOH923 2.1 25.0 1.0
O B:HOH949 2.1 23.9 1.0
CG B:ASP564 3.0 31.6 1.0
OD2 B:ASP564 3.4 36.0 1.0
ZN B:ZN801 3.8 39.4 1.0
O B:HOH970 3.8 43.5 1.0
NE2 B:HIS595 4.1 34.7 1.0
OE2 B:GLU592 4.1 36.5 1.0
CD2 B:HIS563 4.2 31.7 1.0
CD2 B:HIS567 4.3 35.8 1.0
O B:HOH975 4.3 37.5 1.0
O B:HIS563 4.3 34.5 1.0
OG1 B:THR633 4.3 34.2 1.0
CD2 B:HIS595 4.4 38.8 1.0
CB B:ASP564 4.4 31.4 1.0
OD2 B:ASP674 4.4 37.6 1.0
NE2 B:HIS567 4.4 36.7 1.0
CD2 B:HIS525 4.4 37.1 1.0
NE2 B:HIS525 4.5 38.1 1.0
NE2 B:HIS563 4.5 28.9 1.0
O B:THR633 4.6 35.6 1.0
CA B:ASP564 4.7 31.9 1.0
CB B:THR633 4.8 36.6 1.0
CG B:GLU592 4.8 38.0 1.0
CD B:GLU592 4.9 36.8 1.0

Magnesium binding site 3 out of 4 in 5sev

Go back to Magnesium Binding Sites List in 5sev
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:34.5
occ:1.00
 O C:HOH919 2.0 37.0 1.0
O C:HOH950 2.0 35.2 1.0
OD1 C:ASP564 2.0 34.6 1.0
O C:HOH977 2.1 34.8 1.0
O C:HOH924 2.1 29.4 1.0
O C:HOH914 2.2 26.8 1.0
CG C:ASP564 3.0 34.9 1.0
OD2 C:ASP564 3.3 35.2 1.0
O C:HOH973 3.8 41.5 1.0
ZN C:ZN801 3.8 43.1 1.0
O C:HOH992 3.8 54.5 1.0
OE2 C:GLU592 4.0 41.0 1.0
NE2 C:HIS595 4.1 37.8 1.0
CD2 C:HIS567 4.2 39.1 1.0
O C:HIS563 4.3 35.2 1.0
CD2 C:HIS563 4.3 33.5 1.0
CD2 C:HIS595 4.3 36.4 1.0
O C:HOH956 4.4 45.0 1.0
OG1 C:THR633 4.4 36.5 1.0
CB C:ASP564 4.4 32.4 1.0
NE2 C:HIS567 4.4 39.9 1.0
OD2 C:ASP674 4.4 38.2 1.0
O C:THR633 4.5 39.3 1.0
CD2 C:HIS525 4.6 43.2 1.0
NE2 C:HIS563 4.7 35.8 1.0
NE2 C:HIS525 4.7 41.2 1.0
CA C:ASP564 4.8 32.1 1.0
CG C:GLU592 4.8 38.2 1.0
CB C:THR633 4.8 37.2 1.0
CD C:GLU592 4.9 41.9 1.0

Magnesium binding site 4 out of 4 in 5sev

Go back to Magnesium Binding Sites List in 5sev
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine


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 2,3,5- Trimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:44.5
occ:1.00
 O D:HOH919 2.0 39.4 1.0
O D:HOH921 2.1 43.3 1.0
O D:HOH934 2.1 39.3 1.0
O D:HOH913 2.1 42.2 1.0
O D:HOH943 2.2 40.6 1.0
OD1 D:ASP564 2.3 50.2 1.0
CG D:ASP564 3.2 44.8 1.0
OD2 D:ASP564 3.5 56.4 1.0
O D:HOH925 3.8 42.9 1.0
OE2 D:GLU592 3.9 49.3 1.0
ZN D:ZN801 3.9 51.8 1.0
O D:HOH932 4.0 41.9 1.0
NE2 D:HIS595 4.1 48.5 1.0
CD2 D:HIS567 4.3 49.8 1.0
OG1 D:THR633 4.3 45.8 1.0
CD2 D:HIS563 4.4 39.5 1.0
OD2 D:ASP674 4.4 54.5 1.0
CD2 D:HIS595 4.4 52.6 1.0
O D:HIS563 4.4 46.5 1.0
O D:THR633 4.5 47.5 1.0
NE2 D:HIS567 4.5 52.5 1.0
CB D:ASP564 4.5 45.9 1.0
CD2 D:HIS525 4.7 48.8 1.0
NE2 D:HIS525 4.7 53.0 1.0
O D:HOH946 4.7 43.5 1.0
CB D:THR633 4.8 47.2 1.0
NE2 D:HIS563 4.8 41.9 1.0
CD D:GLU592 4.8 53.5 1.0
CA D:ASP564 4.9 43.0 1.0
CG D:GLU592 4.9 50.6 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 03:27:16 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy