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Magnesium in PDB 5sj8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile, PDB code: 5sj8 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) 43.61 / 2.49
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.11, 135.11, 235.005, 90, 90, 120
R / Rfree (%) 16.6 / 20.1

Other elements in 5sj8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile also contains other interesting chemical elements:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile (pdb code 5sj8). 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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile, PDB code: 5sj8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sj8

Go back to Magnesium Binding Sites List in 5sj8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:36.7
occ:1.00
 O A:HOH939 1.9 37.7 1.0
O A:HOH963 2.0 36.1 1.0
O A:HOH906 2.0 36.2 1.0
O A:HOH932 2.1 38.0 1.0
O A:HOH918 2.2 36.1 1.0
OD1 A:ASP564 2.2 38.5 1.0
CG A:ASP564 3.2 41.1 1.0
OD2 A:ASP564 3.5 39.5 1.0
ZN A:ZN801 3.9 42.5 1.0
OE2 A:GLU592 4.0 44.2 1.0
NE2 A:HIS595 4.1 41.0 1.0
CD2 A:HIS567 4.2 44.9 1.0
CD2 A:HIS595 4.4 38.9 1.0
NE2 A:HIS567 4.4 46.2 1.0
OG1 A:THR633 4.4 36.3 1.0
OD2 A:ASP674 4.5 47.1 1.0
O A:THR633 4.5 41.8 1.0
CB A:ASP564 4.5 38.8 1.0
NE2 A:HIS525 4.5 42.7 1.0
CD2 A:HIS525 4.5 42.1 1.0
CD2 A:HIS563 4.6 35.1 1.0
O A:HIS563 4.6 35.2 1.0
O A:HOH953 4.7 39.6 1.0
CG A:GLU592 4.7 41.2 1.0
CB A:THR633 4.7 36.2 1.0
CD A:GLU592 4.8 44.0 1.0
CA A:ASP564 4.9 39.6 1.0
NE2 A:HIS563 4.9 34.3 1.0

Magnesium binding site 2 out of 4 in 5sj8

Go back to Magnesium Binding Sites List in 5sj8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:31.5
occ:1.00
 O B:HOH915 1.9 30.5 1.0
O B:HOH938 1.9 22.5 1.0
O B:HOH904 2.0 21.8 1.0
O B:HOH971 2.1 31.8 1.0
OD1 B:ASP564 2.1 33.9 1.0
O B:HOH944 2.2 24.2 1.0
CG B:ASP564 3.1 33.8 1.0
OD2 B:ASP564 3.5 30.5 1.0
ZN B:ZN801 3.9 38.7 1.0
O B:HOH955 3.9 39.2 1.0
OE2 B:GLU592 3.9 33.4 1.0
NE2 B:HIS595 4.0 34.7 1.0
CD2 B:HIS563 4.2 31.4 1.0
CD2 B:HIS595 4.3 35.7 1.0
CD2 B:HIS567 4.3 40.2 1.0
O B:HOH924 4.4 34.1 1.0
NE2 B:HIS567 4.4 39.5 1.0
OD2 B:ASP674 4.4 42.1 1.0
O B:HIS563 4.4 31.3 1.0
CB B:ASP564 4.4 31.5 1.0
OG1 B:THR633 4.5 37.6 1.0
O B:THR633 4.5 34.7 1.0
NE2 B:HIS563 4.5 31.3 1.0
CD2 B:HIS525 4.7 35.7 1.0
CB B:THR633 4.7 36.2 1.0
NE2 B:HIS525 4.7 34.6 1.0
CA B:ASP564 4.8 33.5 1.0
CD B:GLU592 4.8 35.4 1.0
CG B:GLU592 4.9 36.5 1.0

Magnesium binding site 3 out of 4 in 5sj8

Go back to Magnesium Binding Sites List in 5sj8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:32.2
occ:1.00
 O C:HOH940 1.8 35.9 1.0
OD1 C:ASP564 1.9 35.7 1.0
O C:HOH914 2.0 33.6 1.0
O C:HOH968 2.2 33.9 1.0
O C:HOH916 2.2 30.9 1.0
O C:HOH932 2.3 26.1 1.0
CG C:ASP564 3.0 37.5 1.0
OD2 C:ASP564 3.5 40.1 1.0
ZN C:ZN801 3.9 42.9 1.0
NE2 C:HIS595 3.9 41.0 1.0
O C:HOH941 4.0 45.8 1.0
OE2 C:GLU592 4.0 39.5 1.0
CD2 C:HIS567 4.1 43.5 1.0
CD2 C:HIS595 4.1 42.4 1.0
O C:HIS563 4.2 35.6 1.0
NE2 C:HIS567 4.3 45.1 1.0
CD2 C:HIS563 4.3 35.8 1.0
CB C:ASP564 4.3 31.6 1.0
OG1 C:THR633 4.4 38.8 1.0
OD2 C:ASP674 4.4 34.2 1.0
O C:HOH938 4.5 29.9 1.0
CA C:ASP564 4.6 32.9 1.0
NE2 C:HIS563 4.7 38.7 1.0
CG C:GLU592 4.8 42.1 1.0
O C:THR633 4.8 41.2 1.0
CB C:THR633 4.8 38.7 1.0
CD C:GLU592 4.8 45.8 1.0
CD2 C:HIS525 4.8 39.7 1.0
NE2 C:HIS525 4.8 36.4 1.0
C C:HIS563 5.0 33.8 1.0

Magnesium binding site 4 out of 4 in 5sj8

Go back to Magnesium Binding Sites List in 5sj8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:48.6
occ:1.00
 OD1 D:ASP564 1.9 42.1 1.0
O D:HOH903 1.9 41.4 1.0
O D:HOH909 2.1 40.8 1.0
O D:HOH916 2.1 40.1 1.0
O D:HOH906 2.2 38.3 1.0
O D:HOH925 2.2 37.8 1.0
CG D:ASP564 3.0 45.4 1.0
OD2 D:ASP564 3.4 52.9 1.0
O D:HOH926 3.7 39.1 1.0
ZN D:ZN801 3.8 51.4 1.0
OE2 D:GLU592 3.9 47.9 1.0
NE2 D:HIS595 4.0 52.9 1.0
CD2 D:HIS567 4.1 55.0 1.0
CD2 D:HIS563 4.3 36.1 1.0
CD2 D:HIS595 4.3 52.3 1.0
CB D:ASP564 4.3 41.7 1.0
NE2 D:HIS567 4.3 54.2 1.0
OG1 D:THR633 4.3 45.1 1.0
O D:HIS563 4.4 41.9 1.0
OD2 D:ASP674 4.5 47.0 1.0
CD2 D:HIS525 4.6 53.7 1.0
NE2 D:HIS563 4.6 38.5 1.0
CA D:ASP564 4.6 40.6 1.0
NE2 D:HIS525 4.7 49.9 1.0
O D:THR633 4.7 49.6 1.0
CD D:GLU592 4.7 48.9 1.0
CB D:THR633 4.8 47.3 1.0
CG D:GLU592 4.8 50.8 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: Wed Apr 5 11:34:43 2023

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