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Zinc 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:

Magnesium (Mg) 4 atoms
Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5siw

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:36.3
occ:1.00
 O A:HOH965 2.1 31.7 1.0
NE2 A:HIS529 2.1 29.9 1.0
NE2 A:HIS563 2.2 30.9 1.0
OD2 A:ASP564 2.2 35.8 1.0
O A:HOH979 2.3 45.2 1.0
OD1 A:ASP674 2.3 39.0 1.0
CD2 A:HIS563 3.0 29.3 1.0
CD2 A:HIS529 3.1 28.6 1.0
CG A:ASP674 3.1 36.9 1.0
CG A:ASP564 3.1 34.6 1.0
CE1 A:HIS529 3.2 30.2 1.0
CE1 A:HIS563 3.2 30.9 1.0
OD2 A:ASP674 3.4 37.7 1.0
OD1 A:ASP564 3.6 33.3 1.0
MG A:MG802 3.9 34.4 1.0
O A:HOH993 4.1 29.4 1.0
CD2 A:HIS525 4.1 34.0 1.0
CG A:HIS563 4.2 30.2 1.0
CG A:HIS529 4.2 32.3 1.0
ND1 A:HIS529 4.3 32.1 1.0
O A:HOH962 4.3 47.8 1.0
ND1 A:HIS563 4.3 25.2 1.0
CB A:ASP564 4.3 30.4 1.0
CB A:ASP674 4.5 31.8 1.0
NE2 A:HIS525 4.5 33.8 1.0
O A:HOH918 4.6 23.3 1.0
CG2 A:VAL533 4.6 27.9 1.0
O A:ASP674 4.9 32.6 1.0
CA A:ASP674 4.9 29.2 1.0

Zinc binding site 2 out of 4 in 5siw

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Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:33.2
occ:1.00
 NE2 B:HIS563 2.1 30.0 1.0
O B:HOH944 2.1 27.0 1.0
NE2 B:HIS529 2.2 25.3 1.0
OD2 B:ASP564 2.2 26.1 1.0
OD1 B:ASP674 2.2 28.6 1.0
O B:HOH933 2.8 51.5 1.0
CD2 B:HIS563 3.0 31.3 1.0
CG B:ASP674 3.1 29.4 1.0
CD2 B:HIS529 3.1 32.2 1.0
CE1 B:HIS563 3.1 30.6 1.0
CG B:ASP564 3.2 25.6 1.0
CE1 B:HIS529 3.2 26.6 1.0
OD2 B:ASP674 3.2 32.8 1.0
OD1 B:ASP564 3.6 26.0 1.0
MG B:MG802 3.8 29.8 1.0
CD2 B:HIS525 4.0 28.1 1.0
O B:HOH986 4.1 25.1 1.0
CG B:HIS563 4.2 29.0 1.0
O B:HOH949 4.2 39.9 1.0
ND1 B:HIS563 4.2 27.5 1.0
CG B:HIS529 4.3 30.3 1.0
ND1 B:HIS529 4.3 25.0 1.0
CB B:ASP564 4.4 26.7 1.0
NE2 B:HIS525 4.4 29.1 1.0
CB B:ASP674 4.5 30.1 1.0
O B:HOH931 4.6 31.7 1.0
CG2 B:VAL533 4.7 27.2 1.0
CA B:ASP674 4.8 27.8 1.0
O B:ASP674 4.9 28.4 1.0

Zinc binding site 3 out of 4 in 5siw

Go back to Zinc Binding Sites List in 5siw
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:34.6
occ:1.00
 NE2 C:HIS529 2.1 31.4 1.0
O C:HOH934 2.1 25.7 1.0
OD2 C:ASP564 2.2 31.0 1.0
NE2 C:HIS563 2.2 25.3 1.0
OD1 C:ASP674 2.2 34.1 1.0
O C:HOH932 2.5 48.7 1.0
CD2 C:HIS529 3.1 29.4 1.0
CG C:ASP674 3.1 29.4 1.0
CD2 C:HIS563 3.1 25.0 1.0
CG C:ASP564 3.1 29.4 1.0
CE1 C:HIS529 3.2 34.5 1.0
OD2 C:ASP674 3.2 35.6 1.0
CE1 C:HIS563 3.2 27.5 1.0
OD1 C:ASP564 3.5 31.1 1.0
MG C:MG802 3.8 29.9 1.0
CD2 C:HIS525 4.1 31.8 1.0
O C:HOH990 4.2 27.3 1.0
CG C:HIS529 4.2 27.9 1.0
CG C:HIS563 4.3 27.6 1.0
ND1 C:HIS529 4.3 28.0 1.0
ND1 C:HIS563 4.3 28.5 1.0
CB C:ASP564 4.4 23.6 1.0
O C:HOH984 4.4 43.4 1.0
NE2 C:HIS525 4.4 32.8 1.0
CB C:ASP674 4.5 33.4 1.0
O C:HOH947 4.5 30.7 1.0
O C:HOH1015 4.6 51.3 1.0
CG2 C:VAL533 4.8 28.6 1.0
CA C:ASP674 4.8 33.1 1.0

Zinc binding site 4 out of 4 in 5siw

Go back to Zinc Binding Sites List in 5siw
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:47.3
occ:1.00
 O D:HOH928 1.9 38.3 1.0
NE2 D:HIS529 2.1 41.3 1.0
OD2 D:ASP564 2.2 50.6 1.0
NE2 D:HIS563 2.2 35.7 1.0
OD1 D:ASP674 2.3 44.4 1.0
O D:HOH930 2.4 47.5 1.0
CD2 D:HIS563 3.0 40.0 1.0
CG D:ASP564 3.1 43.8 1.0
CE1 D:HIS529 3.1 43.3 1.0
CD2 D:HIS529 3.1 49.5 1.0
CG D:ASP674 3.1 43.2 1.0
OD2 D:ASP674 3.3 48.1 1.0
CE1 D:HIS563 3.3 43.3 1.0
OD1 D:ASP564 3.5 46.9 1.0
MG D:MG802 3.9 42.8 1.0
O D:HOH948 4.1 44.4 1.0
CD2 D:HIS525 4.1 45.0 1.0
ND1 D:HIS529 4.2 42.0 1.0
CG D:HIS563 4.2 39.3 1.0
CB D:ASP564 4.3 43.6 1.0
CG D:HIS529 4.3 40.9 1.0
O D:HOH921 4.3 57.6 1.0
ND1 D:HIS563 4.4 39.0 1.0
CB D:ASP674 4.5 42.2 1.0
NE2 D:HIS525 4.5 47.4 1.0
CG2 D:VAL533 4.7 46.9 1.0
O D:HOH915 4.7 43.1 1.0
O D:ASP674 4.9 47.0 1.0
CA D:ASP674 4.9 42.8 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 Oct 28 05:52:52 2024

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