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Magnesium in PDB 5si5: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5 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) 43.35 / 2.27
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.764, 134.764, 234.884, 90, 90, 120
R / Rfree (%) 18 / 22.4

Other elements in 5si5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide 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 N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide (pdb code 5si5). 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 N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5si5

Go back to Magnesium Binding Sites List in 5si5
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:30.8
occ:1.00
 O A:HOH990 2.0 26.7 1.0
O A:HOH953 2.0 32.5 1.0
O A:HOH930 2.0 26.2 1.0
O A:HOH954 2.0 25.7 1.0
OD1 A:ASP564 2.1 27.6 1.0
O A:HOH940 2.1 26.5 1.0
CG A:ASP564 3.1 30.0 1.0
OD2 A:ASP564 3.4 28.2 1.0
ZN A:ZN801 3.9 34.0 1.0
O A:HOH970 4.0 27.9 1.0
OE2 A:GLU592 4.0 36.2 1.0
NE2 A:HIS595 4.1 29.0 1.0
CD2 A:HIS567 4.1 32.0 1.0
NE2 A:HIS567 4.2 31.0 1.0
O A:HOH952 4.4 33.7 1.0
CD2 A:HIS563 4.4 28.5 1.0
CD2 A:HIS595 4.4 28.7 1.0
OG1 A:THR633 4.4 27.5 1.0
O A:HIS563 4.5 29.0 1.0
CB A:ASP564 4.5 28.4 1.0
OD2 A:ASP674 4.5 32.6 1.0
NE2 A:HIS525 4.5 30.6 1.0
O A:THR633 4.6 32.0 1.0
CD2 A:HIS525 4.6 30.9 1.0
NE2 A:HIS563 4.7 28.1 1.0
CB A:THR633 4.8 28.1 1.0
CA A:ASP564 4.8 30.1 1.0
CG A:GLU592 4.8 33.7 1.0
CD A:GLU592 4.9 32.2 1.0

Magnesium binding site 2 out of 4 in 5si5

Go back to Magnesium Binding Sites List in 5si5
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:23.1
occ:1.00
 O B:HOH934 2.0 29.3 1.0
O B:HOH931 2.0 22.9 1.0
OD1 B:ASP564 2.0 26.5 1.0
O B:HOH962 2.1 23.3 1.0
O B:HOH987 2.1 17.9 1.0
O B:HOH912 2.1 22.2 1.0
CG B:ASP564 3.0 29.8 1.0
OD2 B:ASP564 3.4 29.4 1.0
ZN B:ZN801 3.8 32.5 1.0
NE2 B:HIS595 4.0 30.5 1.0
OE2 B:GLU592 4.1 31.8 1.0
O B:HOH953 4.2 36.3 1.0
CD2 B:HIS563 4.2 27.5 1.0
OG1 B:THR633 4.2 28.6 1.0
CD2 B:HIS567 4.3 31.5 1.0
OD2 B:ASP674 4.3 31.5 1.0
CD2 B:HIS595 4.3 31.0 1.0
O B:HIS563 4.3 32.5 1.0
CB B:ASP564 4.4 29.8 1.0
NE2 B:HIS567 4.4 33.8 1.0
O B:THR633 4.6 30.2 1.0
NE2 B:HIS563 4.6 25.3 1.0
O B:HOH961 4.7 35.1 1.0
CD2 B:HIS525 4.7 27.7 1.0
CB B:THR633 4.7 29.8 1.0
NE2 B:HIS525 4.7 29.8 1.0
CA B:ASP564 4.7 30.7 1.0
CG B:GLU592 4.9 32.2 1.0
CD B:GLU592 4.9 33.7 1.0

Magnesium binding site 3 out of 4 in 5si5

Go back to Magnesium Binding Sites List in 5si5
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:28.0
occ:1.00
 O C:HOH919 1.9 29.6 1.0
OD1 C:ASP564 2.0 30.4 1.0
O C:HOH920 2.0 22.3 1.0
O C:HOH966 2.1 23.3 1.0
O C:HOH989 2.1 24.6 1.0
O C:HOH937 2.2 25.2 1.0
CG C:ASP564 3.0 31.2 1.0
OD2 C:ASP564 3.3 29.6 1.0
ZN C:ZN801 3.8 35.1 1.0
O C:HOH960 4.1 37.9 1.0
NE2 C:HIS595 4.1 32.9 1.0
OE2 C:GLU592 4.1 34.3 1.0
CD2 C:HIS567 4.1 34.9 1.0
CD2 C:HIS563 4.2 28.9 1.0
OG1 C:THR633 4.2 31.6 1.0
NE2 C:HIS567 4.3 34.3 1.0
CD2 C:HIS595 4.3 31.8 1.0
OD2 C:ASP674 4.3 32.5 1.0
O C:HIS563 4.3 30.2 1.0
CB C:ASP564 4.4 29.9 1.0
O C:HOH952 4.5 40.5 1.0
O C:THR633 4.5 34.8 1.0
NE2 C:HIS563 4.6 30.4 1.0
CB C:THR633 4.7 32.2 1.0
CA C:ASP564 4.7 31.1 1.0
NE2 C:HIS525 4.8 34.4 1.0
CD2 C:HIS525 4.8 34.5 1.0
CG C:GLU592 4.8 34.0 1.0
O C:HOH979 4.9 47.5 1.0
CD C:GLU592 4.9 35.5 1.0

Magnesium binding site 4 out of 4 in 5si5

Go back to Magnesium Binding Sites List in 5si5
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:48.6
occ:1.00
 O D:HOH918 1.9 36.8 1.0
O D:HOH943 2.1 33.9 1.0
O D:HOH938 2.1 36.6 1.0
O D:HOH911 2.1 36.8 1.0
OD1 D:ASP564 2.1 39.3 1.0
O D:HOH923 2.2 38.5 1.0
CG D:ASP564 3.1 41.8 1.0
OD2 D:ASP564 3.4 45.8 1.0
ZN D:ZN801 3.8 48.1 1.0
O D:HOH935 3.8 44.3 1.0
OE2 D:GLU592 4.1 43.6 1.0
NE2 D:HIS595 4.1 41.5 1.0
CD2 D:HIS567 4.1 44.2 1.0
O D:HOH927 4.1 39.9 1.0
CD2 D:HIS563 4.2 35.9 1.0
NE2 D:HIS567 4.2 41.5 1.0
O D:HIS563 4.3 40.1 1.0
OG1 D:THR633 4.3 38.7 1.0
OD2 D:ASP674 4.3 42.8 1.0
CD2 D:HIS595 4.3 43.0 1.0
CB D:ASP564 4.5 40.3 1.0
NE2 D:HIS563 4.6 32.7 1.0
CD2 D:HIS525 4.6 51.8 1.0
O D:THR633 4.6 44.0 1.0
NE2 D:HIS525 4.6 48.4 1.0
CB D:THR633 4.7 41.3 1.0
CA D:ASP564 4.8 40.8 1.0
CG D:GLU592 4.9 40.1 1.0
CD D:GLU592 4.9 43.1 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 04:08:05 2024

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