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Magnesium in PDB 5sfe: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe was solved by C.Joseph, L.Gobbi, 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) 43.75 / 1.86
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.85, 135.85, 235.666, 90, 90, 120
R / Rfree (%) 17.9 / 22.1

Other elements in 5sfe:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 7 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide (pdb code 5sfe). 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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide, PDB code: 5sfe:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sfe

Go back to Magnesium Binding Sites List in 5sfe
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:23.3
occ:1.00
 O A:HOH1042 1.9 25.6 1.0
O A:HOH963 2.0 22.9 1.0
O A:HOH922 2.0 24.0 1.0
OD1 A:ASP564 2.0 24.8 1.0
O A:HOH975 2.1 21.4 1.0
O A:HOH945 2.2 21.9 1.0
CG A:ASP564 3.0 26.0 1.0
OD2 A:ASP564 3.3 25.2 1.0
ZN A:ZN801 3.7 29.4 1.0
O A:HOH1043 3.9 42.8 1.0
O A:HOH1011 4.0 39.6 1.0
OE2 A:GLU592 4.0 27.1 1.0
NE2 A:HIS595 4.1 26.1 1.0
CD2 A:HIS567 4.3 25.3 1.0
OG1 A:THR633 4.3 26.5 1.0
CD2 A:HIS563 4.3 23.9 1.0
O A:HOH1009 4.3 30.9 1.0
O A:HIS563 4.3 26.1 1.0
CD2 A:HIS595 4.4 23.5 1.0
CB A:ASP564 4.4 23.2 1.0
CD2 A:HIS525 4.5 29.0 1.0
NE2 A:HIS567 4.5 25.0 1.0
OD2 A:ASP674 4.5 33.0 1.0
NE2 A:HIS525 4.6 31.2 1.0
O A:THR633 4.6 27.5 1.0
NE2 A:HIS563 4.6 22.7 1.0
CB A:THR633 4.7 25.5 1.0
CA A:ASP564 4.8 24.6 1.0
CG A:GLU592 4.8 27.1 1.0
CD A:GLU592 4.9 26.4 1.0

Magnesium binding site 2 out of 4 in 5sfe

Go back to Magnesium Binding Sites List in 5sfe
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.0
occ:1.00
 O B:HOH961 2.0 23.4 1.0
O B:HOH938 2.0 19.8 1.0
O B:HOH1042 2.1 24.9 1.0
O B:HOH929 2.1 22.8 1.0
OD1 B:ASP564 2.1 23.2 1.0
O B:HOH1012 2.1 19.9 1.0
CG B:ASP564 3.1 23.0 1.0
OD2 B:ASP564 3.4 21.5 1.0
ZN B:ZN801 3.7 27.7 1.0
O B:HOH1060 3.9 37.7 1.0
OE2 B:GLU592 4.0 27.9 1.0
NE2 B:HIS595 4.1 20.2 1.0
O B:HOH990 4.1 35.0 1.0
OG1 B:THR633 4.2 22.6 1.0
CD2 B:HIS563 4.2 22.0 1.0
CD2 B:HIS567 4.3 25.5 1.0
O B:HIS563 4.3 24.9 1.0
CD2 B:HIS595 4.3 23.2 1.0
O B:HOH986 4.3 27.4 1.0
OD2 B:ASP674 4.4 29.6 1.0
CB B:ASP564 4.4 20.4 1.0
NE2 B:HIS567 4.5 22.8 1.0
NE2 B:HIS563 4.5 22.5 1.0
CD2 B:HIS525 4.6 28.5 1.0
O B:THR633 4.6 22.8 1.0
CB B:THR633 4.7 25.7 1.0
NE2 B:HIS525 4.7 30.1 1.0
CG B:GLU592 4.7 25.2 1.0
CA B:ASP564 4.8 20.2 1.0
CD B:GLU592 4.8 24.2 1.0

Magnesium binding site 3 out of 4 in 5sfe

Go back to Magnesium Binding Sites List in 5sfe
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.9
occ:1.00
 O C:HOH945 2.0 20.5 1.0
O C:HOH1050 2.0 25.3 1.0
O C:HOH1004 2.1 24.9 1.0
OD1 C:ASP564 2.1 22.8 1.0
O C:HOH963 2.1 24.5 1.0
O C:HOH952 2.2 23.4 1.0
CG C:ASP564 3.1 26.5 1.0
OD2 C:ASP564 3.4 24.2 1.0
ZN C:ZN801 3.7 28.8 1.0
O C:HOH1046 3.9 39.1 1.0
OE2 C:GLU592 4.0 30.7 1.0
NE2 C:HIS595 4.0 24.1 1.0
O C:HOH991 4.2 39.1 1.0
OG1 C:THR633 4.2 23.0 1.0
O C:HOH1019 4.2 27.5 1.0
CD2 C:HIS563 4.2 20.1 1.0
CD2 C:HIS567 4.3 27.4 1.0
CD2 C:HIS595 4.3 23.0 1.0
O C:HIS563 4.3 23.8 1.0
OD2 C:ASP674 4.4 33.7 1.0
CB C:ASP564 4.4 23.0 1.0
O C:THR633 4.5 26.0 1.0
NE2 C:HIS567 4.5 24.4 1.0
CD2 C:HIS525 4.6 31.6 1.0
NE2 C:HIS563 4.6 23.8 1.0
NE2 C:HIS525 4.7 28.6 1.0
CB C:THR633 4.7 24.1 1.0
CA C:ASP564 4.8 25.1 1.0
CG C:GLU592 4.8 25.9 1.0
CD C:GLU592 4.9 27.2 1.0

Magnesium binding site 4 out of 4 in 5sfe

Go back to Magnesium Binding Sites List in 5sfe
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide


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-N- [2-(3-Fluorophenyl)Imidazo[1,2-A]Pyrimidin-7-Yl]-4-N,4-N,2- Trimethylpyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:33.2
occ:1.00
 O D:HOH989 2.0 31.7 1.0
O D:HOH949 2.1 27.7 1.0
O D:HOH921 2.1 32.4 1.0
OD1 D:ASP564 2.1 34.6 1.0
O D:HOH965 2.1 25.6 1.0
O D:HOH914 2.1 27.1 1.0
CG D:ASP564 3.1 33.2 1.0
OD2 D:ASP564 3.5 32.5 1.0
ZN D:ZN801 3.7 35.6 1.0
O D:HOH987 4.0 38.4 1.0
OE2 D:GLU592 4.0 35.0 1.0
NE2 D:HIS595 4.1 32.5 1.0
OG1 D:THR633 4.2 31.0 1.0
CD2 D:HIS563 4.3 30.4 1.0
CD2 D:HIS595 4.3 30.4 1.0
O D:HOH991 4.3 37.8 1.0
CD2 D:HIS567 4.3 32.7 1.0
O D:HIS563 4.4 31.5 1.0
OD2 D:ASP674 4.4 38.5 1.0
CB D:ASP564 4.5 29.1 1.0
O D:THR633 4.5 38.7 1.0
NE2 D:HIS567 4.6 31.3 1.0
CD2 D:HIS525 4.6 40.8 1.0
CB D:THR633 4.6 34.5 1.0
NE2 D:HIS525 4.6 44.9 1.0
NE2 D:HIS563 4.7 26.4 1.0
CA D:ASP564 4.8 27.5 1.0
CG D:GLU592 4.9 37.4 1.0
CD D:GLU592 4.9 36.4 1.0

Reference:

L.Gobbi, J.Benz, D.Schlatter, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 03:33:08 2024

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