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Magnesium in PDB 5sib: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sib was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.54
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.556, 135.556, 235.636, 90, 90, 120
R / Rfree (%) 17.2 / 24.9

Other elements in 5sib:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

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

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine (pdb code 5sib). 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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sib:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sib

Go back to Magnesium Binding Sites List in 5sib
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:37.9
occ:1.00
 O A:HOH961 1.9 34.8 1.0
O A:HOH942 2.0 34.7 1.0
O A:HOH910 2.0 31.4 1.0
OD1 A:ASP564 2.1 44.6 1.0
O A:HOH950 2.1 39.0 1.0
O A:HOH913 2.3 30.0 1.0
CG A:ASP564 3.0 40.9 1.0
OD2 A:ASP564 3.3 46.2 1.0
ZN A:ZN801 3.7 45.5 1.0
O A:HOH938 3.8 39.5 1.0
O A:HOH940 3.9 36.8 1.0
OE2 A:GLU592 4.1 43.7 1.0
NE2 A:HIS595 4.1 34.6 1.0
OG1 A:THR633 4.3 40.7 1.0
CD2 A:HIS567 4.4 39.5 1.0
O A:HIS563 4.4 35.1 1.0
CB A:ASP564 4.4 34.9 1.0
CD2 A:HIS563 4.4 35.6 1.0
CD2 A:HIS595 4.4 35.5 1.0
O A:THR633 4.4 34.8 1.0
OD2 A:ASP674 4.5 37.4 1.0
NE2 A:HIS525 4.5 36.5 1.0
CD2 A:HIS525 4.5 38.1 1.0
NE2 A:HIS567 4.5 38.6 1.0
NE2 A:HIS563 4.7 32.6 1.0
CB A:THR633 4.7 39.8 1.0
CG A:GLU592 4.9 37.0 1.0
CA A:ASP564 4.9 36.3 1.0
CD A:GLU592 4.9 39.2 1.0

Magnesium binding site 2 out of 4 in 5sib

Go back to Magnesium Binding Sites List in 5sib
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:33.8
occ:1.00
 O B:HOH918 1.9 36.6 1.0
O B:HOH961 1.9 30.4 1.0
O B:HOH952 2.0 23.3 1.0
O B:HOH935 2.1 30.6 1.0
OD1 B:ASP564 2.1 39.9 1.0
O B:HOH910 2.1 23.2 1.0
CG B:ASP564 3.1 39.2 1.0
OD2 B:ASP564 3.5 44.4 1.0
OE2 B:GLU592 3.9 33.5 1.0
ZN B:ZN801 3.9 39.8 1.0
NE2 B:HIS595 3.9 39.7 1.0
O B:HOH942 4.0 33.2 1.0
O B:HOH938 4.1 28.9 1.0
OG1 B:THR633 4.2 35.6 1.0
CD2 B:HIS567 4.2 37.1 1.0
CD2 B:HIS563 4.2 37.0 1.0
CD2 B:HIS595 4.2 40.7 1.0
NE2 B:HIS567 4.3 39.0 1.0
O B:HIS563 4.4 35.3 1.0
CB B:ASP564 4.5 37.2 1.0
O B:THR633 4.5 26.9 1.0
CD2 B:HIS525 4.5 38.3 1.0
NE2 B:HIS563 4.6 35.2 1.0
OD2 B:ASP674 4.6 35.1 1.0
NE2 B:HIS525 4.6 35.0 1.0
CB B:THR633 4.7 35.0 1.0
CD B:GLU592 4.7 36.5 1.0
CG B:GLU592 4.7 35.1 1.0
CA B:ASP564 4.8 38.9 1.0

Magnesium binding site 3 out of 4 in 5sib

Go back to Magnesium Binding Sites List in 5sib
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:35.9
occ:1.00
 O C:HOH929 2.0 24.9 1.0
O C:HOH940 2.0 31.3 1.0
O C:HOH950 2.0 24.3 1.0
O C:HOH960 2.1 22.9 1.0
OD1 C:ASP564 2.1 39.1 1.0
O C:HOH917 2.2 24.4 1.0
CG C:ASP564 3.1 42.2 1.0
OD2 C:ASP564 3.3 49.4 1.0
O C:HOH969 3.7 45.0 1.0
O C:HOH946 3.8 39.1 1.0
ZN C:ZN801 3.8 44.8 1.0
OE2 C:GLU592 3.9 35.1 1.0
NE2 C:HIS595 4.0 41.6 1.0
CD2 C:HIS563 4.2 37.8 1.0
CD2 C:HIS567 4.2 37.7 1.0
O C:HOH936 4.2 27.2 1.0
CD2 C:HIS595 4.3 43.0 1.0
O C:HIS563 4.3 41.1 1.0
NE2 C:HIS567 4.4 42.3 1.0
OG1 C:THR633 4.4 33.9 1.0
CB C:ASP564 4.5 39.8 1.0
OD2 C:ASP674 4.5 35.9 1.0
O C:THR633 4.5 38.4 1.0
NE2 C:HIS563 4.5 39.4 1.0
CB C:THR633 4.6 38.1 1.0
NE2 C:HIS525 4.7 47.8 1.0
CD2 C:HIS525 4.7 48.4 1.0
CD C:GLU592 4.8 41.6 1.0
CG C:GLU592 4.8 39.1 1.0
CA C:ASP564 4.8 41.1 1.0
O C:HOH976 4.9 34.6 1.0

Magnesium binding site 4 out of 4 in 5sib

Go back to Magnesium Binding Sites List in 5sib
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:49.4
occ:1.00
 O D:HOH915 2.0 47.3 1.0
OD1 D:ASP564 2.0 63.0 1.0
O D:HOH901 2.3 43.5 1.0
O D:HOH927 2.3 46.0 1.0
O D:HOH906 2.3 47.4 1.0
O D:HOH918 2.3 38.0 1.0
CG D:ASP564 3.0 67.1 1.0
OD2 D:ASP564 3.4 69.1 1.0
O D:HOH926 3.4 41.3 1.0
ZN D:ZN801 3.9 67.3 1.0
NE2 D:HIS595 3.9 62.6 1.0
O D:HOH907 3.9 43.1 1.0
CD2 D:HIS567 4.0 53.5 1.0
OE2 D:GLU592 4.0 47.2 1.0
NE2 D:HIS567 4.2 54.9 1.0
CD2 D:HIS595 4.3 60.0 1.0
CB D:ASP564 4.3 63.1 1.0
CD2 D:HIS525 4.4 63.7 1.0
O D:HIS563 4.4 61.1 1.0
NE2 D:HIS525 4.4 68.6 1.0
OG1 D:THR633 4.4 52.9 1.0
CD2 D:HIS563 4.5 50.6 1.0
CA D:ASP564 4.7 58.8 1.0
CD D:GLU592 4.8 49.4 1.0
OD2 D:ASP674 4.8 61.7 1.0
NE2 D:HIS563 4.9 50.2 1.0
O D:THR633 4.9 57.2 1.0
CE1 D:HIS595 5.0 60.3 1.0
CG D:GLU592 5.0 51.1 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: Tue Aug 12 19:56:54 2025

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