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Magnesium in PDB 5si4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One, PDB code: 5si4 was solved by C.Joseph, J.Benz, A.Flohr, M.Rogers-Evans, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.39
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.86, 135.86, 235.62, 90, 90, 120
R / Rfree (%) 17.5 / 23.8

Other elements in 5si4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Fluorine (F) 21 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One (pdb code 5si4). 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-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One, PDB code: 5si4:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5si4

Go back to Magnesium Binding Sites List in 5si4
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One


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-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:35.5
occ:1.00
 O A:HOH914 2.0 25.8 1.0
O A:HOH957 2.0 40.8 1.0
O A:HOH908 2.1 30.5 1.0
OD1 A:ASP564 2.1 35.7 1.0
O A:HOH939 2.2 35.4 1.0
O A:HOH917 2.3 33.9 1.0
CG A:ASP564 3.1 34.8 1.0
OD2 A:ASP564 3.3 37.8 1.0
O A:HOH987 3.8 47.3 1.0
ZN A:ZN801 3.9 37.9 1.0
O A:HOH954 3.9 35.6 1.0
OE2 A:GLU592 4.2 36.0 1.0
CD2 A:HIS567 4.2 36.7 1.0
NE2 A:HIS595 4.2 33.1 1.0
OG1 A:THR633 4.3 36.9 1.0
CD2 A:HIS563 4.3 29.9 1.0
OD2 A:ASP674 4.3 44.7 1.0
NE2 A:HIS567 4.3 38.1 1.0
NE2 A:HIS525 4.4 32.6 1.0
CB A:ASP564 4.5 31.6 1.0
C29 A:JLR803 4.5 34.7 0.5
CD2 A:HIS525 4.5 31.7 1.0
O A:HIS563 4.5 31.7 1.0
CD2 A:HIS595 4.6 32.4 1.0
O A:THR633 4.6 31.9 1.0
NE2 A:HIS563 4.6 28.2 1.0
CB A:THR633 4.7 34.8 1.0
C33 A:JLR803 4.7 36.1 0.5
CA A:ASP564 4.9 32.9 1.0
CG A:GLU592 4.9 34.3 1.0
CD A:GLU592 5.0 35.8 1.0
C29 A:JLR803 5.0 32.2 0.5

Magnesium binding site 2 out of 4 in 5si4

Go back to Magnesium Binding Sites List in 5si4
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One


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-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:28.8
occ:1.00
 O B:HOH932 1.9 27.0 1.0
O B:HOH944 2.0 28.5 1.0
O B:HOH924 2.0 24.4 1.0
O B:HOH943 2.1 25.0 1.0
O B:HOH978 2.1 22.9 1.0
OD1 B:ASP564 2.2 30.3 1.0
CG B:ASP564 3.2 30.6 1.0
OD2 B:ASP564 3.6 30.6 1.0
ZN B:ZN801 4.0 34.1 1.0
OE2 B:GLU592 4.0 29.2 1.0
O B:HOH968 4.0 33.4 1.0
OG1 B:THR633 4.1 32.5 1.0
NE2 B:HIS595 4.1 31.7 1.0
O B:HOH974 4.2 31.5 1.0
CD2 B:HIS563 4.3 29.4 1.0
CD2 B:HIS595 4.3 33.6 1.0
CD2 B:HIS567 4.4 35.2 1.0
OD2 B:ASP674 4.4 33.0 1.0
O B:THR633 4.4 28.8 1.0
O B:HIS563 4.4 37.8 1.0
NE2 B:HIS567 4.4 34.8 1.0
CB B:THR633 4.5 32.9 1.0
CB B:ASP564 4.6 30.1 1.0
CG B:GLU592 4.7 32.1 1.0
NE2 B:HIS563 4.7 27.5 1.0
C29 B:JLR803 4.7 39.7 0.5
CD B:GLU592 4.8 30.9 1.0
CD2 B:HIS525 4.8 32.6 1.0
NE2 B:HIS525 4.8 31.9 1.0
CA B:ASP564 4.8 33.3 1.0
C29 B:JLR803 4.9 41.6 0.5
C33 B:JLR803 4.9 40.2 0.5
C33 B:JLR803 4.9 42.5 0.5
C B:THR633 5.0 27.9 1.0

Magnesium binding site 3 out of 4 in 5si4

Go back to Magnesium Binding Sites List in 5si4
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One


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-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.8
occ:1.00
 O C:HOH950 1.9 29.2 1.0
OD1 C:ASP564 2.1 30.2 1.0
O C:HOH1017 2.1 42.1 1.0
O C:HOH981 2.1 28.1 1.0
O C:HOH938 2.2 23.2 1.0
O C:HOH947 2.3 24.8 1.0
CG C:ASP564 3.0 30.3 1.0
OD2 C:ASP564 3.3 31.1 1.0
ZN C:ZN801 3.9 38.2 1.0
NE2 C:HIS595 4.0 40.3 1.0
CD2 C:HIS567 4.0 32.9 1.0
OE2 C:GLU592 4.1 31.5 1.0
O C:HOH976 4.2 39.1 1.0
O C:HOH973 4.2 41.9 1.0
OG1 C:THR633 4.2 30.9 1.0
O C:HIS563 4.2 27.3 1.0
CD2 C:HIS563 4.2 24.6 1.0
NE2 C:HIS567 4.3 34.8 1.0
CD2 C:HIS595 4.3 37.7 1.0
CB C:ASP564 4.4 30.0 1.0
OD2 C:ASP674 4.5 33.1 1.0
NE2 C:HIS563 4.6 25.7 1.0
NE2 C:HIS525 4.6 36.9 1.0
O C:THR633 4.7 31.7 1.0
CA C:ASP564 4.7 29.1 1.0
CB C:THR633 4.7 31.1 1.0
CD2 C:HIS525 4.8 35.3 1.0
C29 C:JLR803 4.8 40.2 0.5
C29 C:JLR803 4.9 39.6 0.5
C33 C:JLR803 4.9 41.1 0.5
CG C:GLU592 4.9 33.0 1.0
C33 C:JLR803 4.9 40.5 0.5
CD C:GLU592 4.9 34.5 1.0

Magnesium binding site 4 out of 4 in 5si4

Go back to Magnesium Binding Sites List in 5si4
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One


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-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:50.2
occ:1.00
 O D:HOH906 1.9 47.7 1.0
O D:HOH919 2.1 33.7 1.0
O D:HOH941 2.1 44.1 1.0
O D:HOH904 2.1 42.4 1.0
OD1 D:ASP564 2.4 45.4 1.0
O D:HOH907 2.4 40.2 1.0
CG D:ASP564 3.3 47.7 1.0
OD2 D:ASP564 3.5 49.2 1.0
O D:HOH933 3.7 37.2 1.0
OE2 D:GLU592 3.8 48.4 1.0
ZN D:ZN801 4.1 55.6 1.0
NE2 D:HIS595 4.1 60.5 1.0
OG1 D:THR633 4.2 45.2 1.0
O D:THR633 4.3 50.1 1.0
CD2 D:HIS567 4.3 46.8 1.0
NE2 D:HIS567 4.4 47.2 1.0
OD2 D:ASP674 4.5 53.8 1.0
CD2 D:HIS595 4.5 54.7 1.0
NE2 D:HIS525 4.5 57.2 1.0
CD2 D:HIS563 4.6 36.7 1.0
CD2 D:HIS525 4.6 53.8 1.0
CB D:ASP564 4.7 48.8 1.0
O D:HIS563 4.7 46.1 1.0
CB D:THR633 4.7 50.7 1.0
C29 D:JLR803 4.7 63.1 1.0
CD D:GLU592 4.7 50.3 1.0
CG D:GLU592 4.9 51.7 1.0
NE2 D:HIS563 4.9 37.0 1.0
C33 D:JLR803 4.9 67.9 1.0
C D:THR633 5.0 50.1 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: Mon Sep 30 04:06:10 2024

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