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Magnesium in PDB 5sef: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sef was solved by C.Joseph, C.Lerner, 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) 43.82 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.272, 135.272, 236.018, 90, 90, 120
R / Rfree (%) 17.2 / 23.2

Other elements in 5sef:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine 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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5sef). 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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sef:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sef

Go back to Magnesium Binding Sites List in 5sef
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:38.5
occ:1.00
 OD1 A:ASP564 2.0 39.3 1.0
O A:HOH948 2.0 36.6 1.0
O A:HOH959 2.0 31.0 1.0
O A:HOH909 2.1 30.2 1.0
O A:HOH935 2.1 35.3 1.0
O A:HOH917 2.1 39.9 1.0
CG A:ASP564 3.0 37.1 1.0
OD2 A:ASP564 3.4 43.5 1.0
ZN A:ZN802 3.8 46.8 1.0
O A:HOH953 3.8 42.7 1.0
NE2 A:HIS595 4.0 39.6 1.0
OE2 A:GLU592 4.0 44.6 1.0
O A:HOH944 4.0 37.4 1.0
O A:HIS563 4.3 40.9 1.0
CD2 A:HIS567 4.3 38.7 1.0
CD2 A:HIS595 4.3 38.4 1.0
CB A:ASP564 4.4 33.1 1.0
CD2 A:HIS563 4.4 41.6 1.0
OG1 A:THR633 4.4 42.9 1.0
CD2 A:HIS525 4.5 41.4 1.0
NE2 A:HIS525 4.5 43.0 1.0
O A:THR633 4.6 43.2 1.0
NE2 A:HIS567 4.6 37.2 1.0
OD2 A:ASP674 4.7 43.5 1.0
CA A:ASP564 4.8 38.7 1.0
NE2 A:HIS563 4.8 36.4 1.0
CB A:THR633 4.8 39.9 1.0
CD A:GLU592 4.9 42.7 1.0
CG A:GLU592 4.9 43.6 1.0

Magnesium binding site 2 out of 4 in 5sef

Go back to Magnesium Binding Sites List in 5sef
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:36.4
occ:1.00
 O B:HOH943 1.9 29.9 1.0
O B:HOH925 2.0 37.1 1.0
O B:HOH928 2.0 33.9 1.0
O B:HOH944 2.0 29.7 1.0
O B:HOH911 2.0 32.0 1.0
OD1 B:ASP564 2.1 35.7 1.0
CG B:ASP564 3.1 38.3 1.0
OD2 B:ASP564 3.5 40.6 1.0
ZN B:ZN802 3.8 44.2 1.0
NE2 B:HIS595 4.0 41.0 1.0
O B:HOH922 4.0 43.7 1.0
O B:HOH948 4.0 44.8 1.0
OE2 B:GLU592 4.1 42.3 1.0
OG1 B:THR633 4.1 42.3 1.0
CD2 B:HIS563 4.3 39.5 1.0
CD2 B:HIS595 4.3 46.0 1.0
CD2 B:HIS567 4.4 39.4 1.0
O B:HIS563 4.4 43.0 1.0
OD2 B:ASP674 4.5 38.9 1.0
CB B:ASP564 4.5 36.1 1.0
CD2 B:HIS525 4.5 42.5 1.0
O B:THR633 4.5 42.2 1.0
NE2 B:HIS567 4.5 40.0 1.0
NE2 B:HIS525 4.6 45.2 1.0
NE2 B:HIS563 4.6 36.1 1.0
CB B:THR633 4.7 42.2 1.0
CG B:GLU592 4.7 39.8 1.0
CA B:ASP564 4.8 40.2 1.0
CD B:GLU592 4.8 40.4 1.0

Magnesium binding site 3 out of 4 in 5sef

Go back to Magnesium Binding Sites List in 5sef
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:38.2
occ:1.00
 O C:HOH929 2.0 39.9 1.0
OD1 C:ASP564 2.0 40.1 1.0
O C:HOH917 2.0 32.3 1.0
O C:HOH948 2.1 32.7 1.0
O C:HOH933 2.1 33.4 1.0
O C:HOH964 2.2 34.4 1.0
CG C:ASP564 3.0 36.8 1.0
OD2 C:ASP564 3.4 44.2 1.0
ZN C:ZN802 3.7 44.3 1.0
O C:HOH954 4.0 45.7 1.0
CD2 C:HIS563 4.1 38.3 1.0
NE2 C:HIS595 4.1 43.1 1.0
OE2 C:GLU592 4.2 43.6 1.0
OG1 C:THR633 4.2 35.5 1.0
O C:HIS563 4.3 35.9 1.0
O C:HOH934 4.3 41.4 1.0
OD2 C:ASP674 4.3 40.9 1.0
CD2 C:HIS567 4.3 42.2 1.0
CD2 C:HIS595 4.4 45.8 1.0
CB C:ASP564 4.4 35.1 1.0
NE2 C:HIS563 4.5 34.9 1.0
CB C:THR633 4.5 39.9 1.0
O C:THR633 4.5 40.8 1.0
NE2 C:HIS567 4.7 39.3 1.0
CD2 C:HIS525 4.7 43.6 1.0
NE2 C:HIS525 4.7 46.6 1.0
CA C:ASP564 4.8 34.3 1.0
CG C:GLU592 4.9 41.1 1.0
CD C:GLU592 5.0 41.9 1.0

Magnesium binding site 4 out of 4 in 5sef

Go back to Magnesium Binding Sites List in 5sef
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,7,8- Trimethyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- [1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:54.2
occ:1.00
 O D:HOH904 2.0 48.4 1.0
O D:HOH902 2.1 53.9 1.0
O D:HOH915 2.1 45.1 1.0
OD1 D:ASP564 2.2 57.6 1.0
O D:HOH906 2.2 57.9 1.0
O D:HOH912 2.3 50.6 1.0
CG D:ASP564 3.1 54.6 1.0
OD2 D:ASP564 3.3 69.1 1.0
ZN D:ZN802 3.8 62.2 1.0
O D:HOH911 3.8 56.1 1.0
OE2 D:GLU592 4.0 61.5 1.0
NE2 D:HIS595 4.2 62.3 1.0
CD2 D:HIS567 4.2 54.1 1.0
CD2 D:HIS525 4.3 66.3 1.0
OG1 D:THR633 4.3 63.5 1.0
NE2 D:HIS525 4.4 64.2 1.0
O D:HIS563 4.4 61.9 1.0
NE2 D:HIS567 4.4 60.5 1.0
CB D:ASP564 4.4 56.0 1.0
CD2 D:HIS563 4.4 61.8 1.0
CD2 D:HIS595 4.5 64.7 1.0
O D:THR633 4.6 62.5 1.0
OD2 D:ASP674 4.6 72.8 1.0
NE2 D:HIS563 4.8 50.9 1.0
CA D:ASP564 4.8 53.7 1.0
CB D:THR633 4.8 68.0 1.0
CD D:GLU592 4.9 58.1 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: Tue Aug 12 19:19:19 2025

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