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Magnesium in PDB 5siw: 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine

Enzymatic activity of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine

All present enzymatic activity of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5siw was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.39 / 2.13
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.88, 134.88, 235.159, 90, 90, 120
R / Rfree (%) 17 / 22.5

Other elements in 5siw:

The structure of 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 12 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5siw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5siw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5siw

Go back to Magnesium Binding Sites List in 5siw
Magnesium binding site 1 out of 4 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[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 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.4
occ:1.00
 O A:HOH993 1.9 29.4 1.0
O A:HOH918 2.0 23.3 1.0
O A:HOH965 2.0 31.7 1.0
O A:HOH947 2.1 29.3 1.0
OD1 A:ASP564 2.1 33.3 1.0
O A:HOH928 2.1 32.8 1.0
CG A:ASP564 3.1 34.6 1.0
OD2 A:ASP564 3.5 35.8 1.0
O A:HOH979 3.9 45.2 1.0
ZN A:ZN801 3.9 36.3 1.0
NE2 A:HIS595 4.0 29.9 1.0
OE2 A:GLU592 4.0 35.2 1.0
O A:HOH973 4.1 33.9 1.0
OG1 A:THR633 4.2 35.8 1.0
O A:HIS563 4.3 30.5 1.0
CD2 A:HIS595 4.3 27.6 1.0
CD2 A:HIS563 4.4 29.3 1.0
CD2 A:HIS567 4.4 33.0 1.0
O A:THR633 4.5 31.5 1.0
CB A:ASP564 4.5 30.4 1.0
OD2 A:ASP674 4.6 37.7 1.0
CD2 A:HIS525 4.6 34.0 1.0
NE2 A:HIS567 4.6 30.3 1.0
NE2 A:HIS563 4.7 30.9 1.0
CB A:THR633 4.7 33.0 1.0
CG A:GLU592 4.7 32.2 1.0
NE2 A:HIS525 4.8 33.8 1.0
CA A:ASP564 4.8 32.6 1.0
CD A:GLU592 4.8 36.0 1.0

Magnesium binding site 2 out of 4 in 5siw

Go back to Magnesium Binding Sites List in 5siw
Magnesium binding site 2 out of 4 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[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 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.8
occ:1.00
 O B:HOH986 2.0 25.1 1.0
O B:HOH944 2.0 27.0 1.0
O B:HOH931 2.1 31.7 1.0
O B:HOH948 2.1 26.3 1.0
O B:HOH904 2.1 27.1 1.0
OD1 B:ASP564 2.1 26.0 1.0
CG B:ASP564 3.2 25.6 1.0
OD2 B:ASP564 3.5 26.1 1.0
ZN B:ZN801 3.8 33.2 1.0
OE2 B:GLU592 4.0 31.9 1.0
NE2 B:HIS595 4.0 28.0 1.0
O B:HOH968 4.0 30.7 1.0
O B:HOH933 4.1 51.5 1.0
CD2 B:HIS567 4.2 24.8 1.0
OG1 B:THR633 4.2 27.0 1.0
CD2 B:HIS563 4.3 31.3 1.0
O B:HIS563 4.3 31.9 1.0
CD2 B:HIS595 4.4 31.2 1.0
NE2 B:HIS567 4.4 25.7 1.0
OD2 B:ASP674 4.5 32.8 1.0
CD2 B:HIS525 4.5 28.1 1.0
CB B:ASP564 4.5 26.7 1.0
NE2 B:HIS563 4.6 30.0 1.0
O B:THR633 4.6 29.2 1.0
NE2 B:HIS525 4.6 29.1 1.0
CB B:THR633 4.7 28.6 1.0
CD B:GLU592 4.8 28.4 1.0
CA B:ASP564 4.8 29.6 1.0
CG B:GLU592 4.8 27.1 1.0

Magnesium binding site 3 out of 4 in 5siw

Go back to Magnesium Binding Sites List in 5siw
Magnesium binding site 3 out of 4 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[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 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.9
occ:1.00
 OD1 C:ASP564 2.0 31.1 1.0
O C:HOH967 2.0 27.7 1.0
O C:HOH947 2.0 30.7 1.0
O C:HOH934 2.0 25.7 1.0
O C:HOH937 2.1 28.0 1.0
O C:HOH990 2.2 27.3 1.0
CG C:ASP564 3.1 29.4 1.0
OD2 C:ASP564 3.5 31.0 1.0
ZN C:ZN801 3.8 34.6 1.0
O C:HOH1015 3.9 51.3 1.0
OE2 C:GLU592 3.9 33.6 1.0
O C:HOH932 3.9 48.7 1.0
NE2 C:HIS595 4.0 31.8 1.0
O C:HOH959 4.1 33.2 1.0
CD2 C:HIS567 4.2 30.4 1.0
CD2 C:HIS563 4.3 25.0 1.0
OG1 C:THR633 4.3 30.8 1.0
O C:HIS563 4.3 30.0 1.0
CD2 C:HIS595 4.4 31.2 1.0
CB C:ASP564 4.4 23.6 1.0
OD2 C:ASP674 4.4 35.6 1.0
NE2 C:HIS567 4.5 31.6 1.0
CD2 C:HIS525 4.6 31.8 1.0
O C:THR633 4.6 36.1 1.0
CB C:THR633 4.6 30.1 1.0
NE2 C:HIS563 4.7 25.3 1.0
NE2 C:HIS525 4.7 32.8 1.0
CA C:ASP564 4.7 29.2 1.0
CG C:GLU592 4.8 30.8 1.0
CD C:GLU592 4.8 32.2 1.0

Magnesium binding site 4 out of 4 in 5siw

Go back to Magnesium Binding Sites List in 5siw
Magnesium binding site 4 out of 4 in the 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[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 5-Methyl-2-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-8- (Trifluoromethyl)-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:42.8
occ:1.00
 OD1 D:ASP564 2.0 46.9 1.0
O D:HOH948 2.0 44.4 1.0
O D:HOH936 2.1 41.7 1.0
O D:HOH915 2.1 43.1 1.0
O D:HOH901 2.2 44.0 1.0
O D:HOH928 2.3 38.3 1.0
CG D:ASP564 3.1 43.8 1.0
OD2 D:ASP564 3.5 50.6 1.0
ZN D:ZN801 3.9 47.3 1.0
NE2 D:HIS595 3.9 44.8 1.0
OE2 D:GLU592 3.9 51.0 1.0
O D:HOH925 3.9 46.3 1.0
O D:HOH930 4.0 47.5 1.0
CD2 D:HIS567 4.1 44.7 1.0
OG1 D:THR633 4.3 43.7 1.0
CD2 D:HIS595 4.3 42.5 1.0
O D:HIS563 4.3 46.0 1.0
CB D:ASP564 4.4 43.6 1.0
NE2 D:HIS567 4.4 46.0 1.0
CD2 D:HIS563 4.4 40.0 1.0
CD2 D:HIS525 4.5 45.0 1.0
OD2 D:ASP674 4.6 48.1 1.0
NE2 D:HIS525 4.6 47.4 1.0
O D:THR633 4.7 44.5 1.0
CA D:ASP564 4.7 43.7 1.0
CD D:GLU592 4.8 46.6 1.0
NE2 D:HIS563 4.9 35.7 1.0
CB D:THR633 4.9 44.4 1.0
CE1 D:HIS595 4.9 46.7 1.0
CG D:GLU592 5.0 49.7 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 04:15:55 2024

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