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Magnesium in PDB 5sgx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sgx was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.72 / 1.93
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.599, 135.599, 235.562, 90, 90, 120
R / Rfree (%) 16.8 / 21.6

Other elements in 5sgx:

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

Magnesium binding site 1 out of 4 in 5sgx

Go back to Magnesium Binding Sites List in 5sgx
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-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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:Mg802

b:26.9
occ:1.00
 O A:HOH934 2.0 23.3 1.0
O A:HOH1031 2.0 23.5 1.0
OD1 A:ASP564 2.0 23.1 1.0
O A:HOH988 2.1 24.8 1.0
O A:HOH968 2.2 25.6 1.0
O A:HOH935 2.2 23.5 1.0
CG A:ASP564 3.1 25.7 1.0
OD2 A:ASP564 3.4 25.9 1.0
ZN A:ZN801 3.8 29.7 1.0
O A:HOH994 3.9 38.4 1.0
OE2 A:GLU592 4.1 27.9 1.0
NE2 A:HIS595 4.1 25.4 1.0
O A:HOH1084 4.1 44.4 1.0
OG1 A:THR633 4.3 25.9 1.0
CD2 A:HIS567 4.3 26.1 1.0
O A:HIS563 4.3 27.1 1.0
O A:HOH1006 4.3 29.1 1.0
CD2 A:HIS595 4.4 23.4 1.0
CD2 A:HIS563 4.4 21.8 1.0
CB A:ASP564 4.4 25.4 1.0
O A:THR633 4.5 26.3 1.0
NE2 A:HIS567 4.5 24.4 1.0
CD2 A:HIS525 4.5 27.7 1.0
NE2 A:HIS525 4.6 28.7 1.0
OD2 A:ASP674 4.6 30.6 1.0
CA A:ASP564 4.8 24.5 1.0
CB A:THR633 4.8 25.7 1.0
NE2 A:HIS563 4.8 23.8 1.0
CG A:GLU592 4.8 28.7 1.0
CD A:GLU592 4.9 29.4 1.0

Magnesium binding site 2 out of 4 in 5sgx

Go back to Magnesium Binding Sites List in 5sgx
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-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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:Mg802

b:23.9
occ:1.00
 O B:HOH970 2.0 20.6 1.0
O B:HOH933 2.0 24.0 1.0
OD1 B:ASP564 2.1 23.5 1.0
O B:HOH918 2.1 21.6 1.0
O B:HOH1021 2.1 19.6 1.0
O B:HOH1019 2.1 22.2 1.0
CG B:ASP564 3.1 20.9 1.0
OD2 B:ASP564 3.4 20.4 1.0
ZN B:ZN801 3.7 27.5 1.0
O B:HOH922 3.9 42.1 1.0
OE2 B:GLU592 4.0 29.4 1.0
NE2 B:HIS595 4.1 23.2 1.0
O B:HOH1105 4.1 38.8 1.0
OG1 B:THR633 4.2 23.1 1.0
O B:HOH995 4.2 25.7 1.0
CD2 B:HIS563 4.3 21.8 1.0
CD2 B:HIS567 4.3 25.4 1.0
O B:HIS563 4.3 27.5 1.0
CD2 B:HIS595 4.4 22.4 1.0
CB B:ASP564 4.4 22.2 1.0
OD2 B:ASP674 4.5 27.3 1.0
CD2 B:HIS525 4.5 24.5 1.0
NE2 B:HIS567 4.5 21.9 1.0
NE2 B:HIS525 4.6 32.0 1.0
NE2 B:HIS563 4.6 22.2 1.0
O B:THR633 4.6 23.4 1.0
CB B:THR633 4.7 25.2 1.0
CA B:ASP564 4.8 21.6 1.0
CG B:GLU592 4.8 24.3 1.0
CD B:GLU592 4.8 25.6 1.0

Magnesium binding site 3 out of 4 in 5sgx

Go back to Magnesium Binding Sites List in 5sgx
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-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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:Mg802

b:25.1
occ:1.00
 OD1 C:ASP564 2.0 26.5 1.0
O C:HOH1001 2.0 25.7 1.0
O C:HOH956 2.1 24.4 1.0
O C:HOH1052 2.1 23.3 1.0
O C:HOH923 2.1 22.5 1.0
O C:HOH946 2.2 23.0 1.0
CG C:ASP564 3.1 24.8 1.0
OD2 C:ASP564 3.4 24.7 1.0
ZN C:ZN801 3.8 28.5 1.0
O C:HOH967 3.9 40.2 1.0
OE2 C:GLU592 4.0 28.4 1.0
NE2 C:HIS595 4.1 27.1 1.0
O C:HOH1098 4.1 41.0 1.0
OG1 C:THR633 4.2 24.3 1.0
CD2 C:HIS567 4.3 25.8 1.0
O C:HOH1022 4.3 26.8 1.0
CD2 C:HIS563 4.3 24.0 1.0
OD2 C:ASP674 4.4 32.0 1.0
O C:HIS563 4.4 24.8 1.0
CB C:ASP564 4.4 24.2 1.0
CD2 C:HIS595 4.5 27.0 1.0
O C:THR633 4.5 25.9 1.0
CD2 C:HIS525 4.5 27.5 1.0
NE2 C:HIS567 4.5 24.9 1.0
NE2 C:HIS525 4.6 28.1 1.0
NE2 C:HIS563 4.7 23.9 1.0
CB C:THR633 4.7 25.6 1.0
CA C:ASP564 4.8 23.6 1.0
CD C:GLU592 4.9 26.2 1.0
CG C:GLU592 4.9 25.2 1.0

Magnesium binding site 4 out of 4 in 5sgx

Go back to Magnesium Binding Sites List in 5sgx
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-[(2R)-2-(Trifluoromethyl)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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)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:Mg802

b:34.2
occ:1.00
 O D:HOH928 2.1 29.8 1.0
O D:HOH938 2.1 25.9 1.0
O D:HOH920 2.1 30.9 1.0
O D:HOH959 2.1 27.8 1.0
O D:HOH942 2.2 27.0 1.0
OD1 D:ASP564 2.2 30.6 1.0
CG D:ASP564 3.2 28.5 1.0
OD2 D:ASP564 3.6 33.8 1.0
O D:HOH955 3.8 41.4 1.0
ZN D:ZN801 3.8 34.3 1.0
OE2 D:GLU592 4.0 34.5 1.0
NE2 D:HIS595 4.1 35.0 1.0
O D:HOH964 4.1 34.6 1.0
OG1 D:THR633 4.2 33.4 1.0
CD2 D:HIS567 4.3 35.1 1.0
OD2 D:ASP674 4.4 34.2 1.0
CD2 D:HIS563 4.4 31.4 1.0
O D:HIS563 4.4 31.3 1.0
CD2 D:HIS595 4.4 33.4 1.0
CD2 D:HIS525 4.5 35.7 1.0
NE2 D:HIS567 4.5 34.0 1.0
NE2 D:HIS525 4.5 40.5 1.0
O D:THR633 4.6 35.9 1.0
CB D:ASP564 4.6 29.8 1.0
CB D:THR633 4.7 34.8 1.0
NE2 D:HIS563 4.8 28.2 1.0
CD D:GLU592 4.9 35.1 1.0
O D:HOH1006 4.9 34.0 1.0
CA D:ASP564 5.0 27.3 1.0
CG D:GLU592 5.0 37.9 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 03:52:20 2024

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