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Magnesium in PDB 5sfs: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfs 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) 43.61 / 2.24
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.57, 135.57, 235.303, 90, 90, 120
R / Rfree (%) 18.8 / 25.2

Other elements in 5sfs:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine (pdb code 5sfs). 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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine, PDB code: 5sfs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfs

Go back to Magnesium Binding Sites List in 5sfs
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:44.6
occ:1.00
 O A:HOH936 2.0 37.3 1.0
O A:HOH911 2.0 43.1 1.0
O A:HOH958 2.0 32.0 1.0
O A:HOH917 2.1 37.8 1.0
OD1 A:ASP564 2.2 32.2 1.0
O A:HOH921 2.3 36.5 1.0
CG A:ASP564 3.2 35.7 1.0
OD2 A:ASP564 3.5 39.6 1.0
O A:HOH948 3.8 38.2 1.0
NE2 A:HIS595 4.0 43.0 1.0
ZN A:ZN801 4.0 44.5 1.0
OE2 A:GLU592 4.0 41.1 1.0
CD2 A:HIS567 4.3 41.0 1.0
O A:THR633 4.3 45.1 1.0
CD2 A:HIS595 4.3 38.0 1.0
OG1 A:THR633 4.3 43.1 1.0
O A:HIS563 4.3 36.3 1.0
NE2 A:HIS567 4.4 37.8 1.0
CD2 A:HIS563 4.5 40.4 1.0
CB A:ASP564 4.5 35.9 1.0
CB A:THR633 4.6 43.1 1.0
OD2 A:ASP674 4.7 49.4 1.0
NE2 A:HIS525 4.7 47.1 1.0
CG A:GLU592 4.7 43.8 1.0
CD2 A:HIS525 4.8 48.5 1.0
NE2 A:HIS563 4.8 39.1 1.0
CD A:GLU592 4.8 47.8 1.0
CA A:ASP564 4.9 39.1 1.0

Magnesium binding site 2 out of 4 in 5sfs

Go back to Magnesium Binding Sites List in 5sfs
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:36.1
occ:1.00
 O B:HOH954 1.9 31.0 1.0
O B:HOH952 1.9 32.6 1.0
O B:HOH945 2.0 40.5 1.0
O B:HOH904 2.0 32.2 1.0
O B:HOH935 2.1 32.8 1.0
OD1 B:ASP564 2.1 34.6 1.0
CG B:ASP564 3.1 32.9 1.0
OD2 B:ASP564 3.4 36.3 1.0
O B:HOH948 3.8 46.5 1.0
ZN B:ZN801 3.8 41.8 1.0
OE2 B:GLU592 3.9 43.4 1.0
NE2 B:HIS595 4.1 30.5 1.0
CD2 B:HIS563 4.1 38.2 1.0
CD2 B:HIS567 4.3 39.9 1.0
CD2 B:HIS525 4.4 37.9 1.0
OG1 B:THR633 4.4 39.5 1.0
O B:HIS563 4.4 40.9 1.0
CD2 B:HIS595 4.4 38.7 1.0
CB B:ASP564 4.4 31.3 1.0
NE2 B:HIS563 4.5 35.7 1.0
O B:THR633 4.5 42.8 1.0
OD2 B:ASP674 4.5 41.3 1.0
NE2 B:HIS525 4.6 39.4 1.0
NE2 B:HIS567 4.6 41.0 1.0
CG B:GLU592 4.7 38.3 1.0
CB B:THR633 4.7 39.1 1.0
CD B:GLU592 4.8 41.5 1.0
CA B:ASP564 4.8 34.7 1.0

Magnesium binding site 3 out of 4 in 5sfs

Go back to Magnesium Binding Sites List in 5sfs
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:37.5
occ:1.00
 O C:HOH931 1.9 33.8 1.0
O C:HOH936 2.0 33.4 1.0
O C:HOH958 2.0 41.4 1.0
OD1 C:ASP564 2.0 35.3 1.0
O C:HOH967 2.2 42.0 1.0
O C:HOH925 2.2 26.1 1.0
CG C:ASP564 3.1 33.2 1.0
OD2 C:ASP564 3.5 33.3 1.0
O C:HOH940 3.7 51.8 1.0
ZN C:ZN801 3.8 44.7 1.0
OE2 C:GLU592 4.0 40.4 1.0
NE2 C:HIS595 4.1 36.7 1.0
OG1 C:THR633 4.2 35.2 1.0
CD2 C:HIS563 4.2 37.9 1.0
CD2 C:HIS567 4.3 37.6 1.0
CD2 C:HIS595 4.3 39.4 1.0
O C:HOH938 4.4 34.9 1.0
CB C:ASP564 4.4 31.4 1.0
OD2 C:ASP674 4.4 43.3 1.0
O C:HIS563 4.4 41.0 1.0
O C:THR633 4.5 36.0 1.0
NE2 C:HIS567 4.5 44.4 1.0
CD2 C:HIS525 4.6 42.0 1.0
NE2 C:HIS525 4.6 42.4 1.0
NE2 C:HIS563 4.7 36.6 1.0
CB C:THR633 4.7 38.0 1.0
CA C:ASP564 4.7 35.8 1.0
CD C:GLU592 4.9 39.9 1.0
CG C:GLU592 4.9 37.8 1.0
O C:HOH971 5.0 33.2 1.0

Magnesium binding site 4 out of 4 in 5sfs

Go back to Magnesium Binding Sites List in 5sfs
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(3S)-3-Methylpyrrolidin-1-Yl]-1,2,4- Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-A]Pyrazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:50.4
occ:1.00
 O D:HOH908 2.0 38.3 1.0
OD1 D:ASP564 2.0 44.6 1.0
O D:HOH921 2.0 32.9 1.0
O D:HOH924 2.2 41.8 1.0
O D:HOH905 2.2 46.4 1.0
O D:HOH930 2.3 41.7 1.0
CG D:ASP564 3.1 41.5 1.0
OD2 D:ASP564 3.5 48.1 1.0
O D:HOH934 3.8 51.4 1.0
OE2 D:GLU592 3.9 48.6 1.0
NE2 D:HIS595 3.9 48.8 1.0
ZN D:ZN801 3.9 50.6 1.0
CD2 D:HIS595 4.2 48.4 1.0
CD2 D:HIS567 4.2 49.4 1.0
OG1 D:THR633 4.3 44.4 1.0
O D:HOH922 4.3 48.4 1.0
CD2 D:HIS563 4.4 40.0 1.0
CB D:ASP564 4.4 40.2 1.0
NE2 D:HIS567 4.4 45.6 1.0
O D:HIS563 4.4 48.4 1.0
CD2 D:HIS525 4.6 51.1 1.0
OD2 D:ASP674 4.7 50.9 1.0
NE2 D:HIS525 4.7 56.6 1.0
NE2 D:HIS563 4.7 38.7 1.0
O D:THR633 4.7 47.7 1.0
CA D:ASP564 4.8 42.7 1.0
CB D:THR633 4.8 45.0 1.0
CD D:GLU592 4.9 49.5 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 03:38:54 2024

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