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

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One, PDB code: 5sgz was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.979, 134.979, 235.207, 90, 90, 120
R / Rfree (%) 18.8 / 22.3

Other elements in 5sgz:

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

Chlorine (Cl) 4 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 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One (pdb code 5sgz). 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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One, PDB code: 5sgz:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgz

Go back to Magnesium Binding Sites List in 5sgz
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.2
occ:1.00
 OD1 A:ASP564 1.9 30.3 1.0
O A:HOH943 2.0 29.3 1.0
O A:HOH987 2.0 28.0 1.0
O A:HOH960 2.1 30.9 1.0
O A:HOH911 2.2 32.3 1.0
O A:HOH939 2.3 37.6 1.0
CG A:ASP564 2.9 28.6 1.0
OD2 A:ASP564 3.2 26.4 1.0
ZN A:ZN801 3.8 34.0 1.0
NE2 A:HIS595 4.0 30.1 1.0
CD2 A:HIS563 4.1 26.7 1.0
O A:HOH955 4.2 36.5 1.0
OE2 A:GLU592 4.2 41.8 1.0
O A:HIS563 4.2 33.6 1.0
CD2 A:HIS567 4.2 33.8 1.0
CD2 A:HIS595 4.2 31.4 1.0
CB A:ASP564 4.3 26.4 1.0
O A:HOH989 4.3 43.9 1.0
NE2 A:HIS567 4.3 32.8 1.0
OG1 A:THR633 4.4 34.6 1.0
NE2 A:HIS563 4.5 28.8 1.0
OD2 A:ASP674 4.5 28.8 1.0
O A:THR633 4.6 35.5 1.0
CA A:ASP564 4.6 30.9 1.0
CD2 A:HIS525 4.7 34.2 1.0
CB A:THR633 4.7 29.4 1.0
NE2 A:HIS525 4.8 32.3 1.0
CG A:GLU592 4.8 36.6 1.0
CD A:GLU592 4.9 40.7 1.0
C A:HIS563 4.9 32.6 1.0

Magnesium binding site 2 out of 4 in 5sgz

Go back to Magnesium Binding Sites List in 5sgz
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:31.3
occ:1.00
 O B:HOH912 2.0 28.7 1.0
O B:HOH922 2.1 23.3 1.0
OD1 B:ASP564 2.1 29.6 1.0
O B:HOH974 2.1 28.9 1.0
O B:HOH963 2.1 23.2 1.0
O B:HOH915 2.2 30.5 1.0
CG B:ASP564 3.2 32.5 1.0
OD2 B:ASP564 3.5 28.7 1.0
ZN B:ZN801 3.9 34.0 1.0
OE2 B:GLU592 4.0 34.5 1.0
O B:HOH977 4.1 34.4 1.0
NE2 B:HIS595 4.2 36.2 1.0
OG1 B:THR633 4.2 35.6 1.0
CD2 B:HIS567 4.3 33.9 1.0
CD2 B:HIS563 4.3 26.5 1.0
OD2 B:ASP674 4.3 38.3 1.0
O B:THR633 4.3 35.2 1.0
NE2 B:HIS567 4.3 33.6 1.0
CD2 B:HIS595 4.4 33.5 1.0
O B:HOH988 4.4 43.0 1.0
O B:HIS563 4.4 32.3 1.0
CB B:ASP564 4.5 30.6 1.0
NE2 B:HIS563 4.6 24.3 1.0
CD2 B:HIS525 4.7 36.1 1.0
NE2 B:HIS525 4.8 34.5 1.0
CG B:GLU592 4.8 30.3 1.0
CB B:THR633 4.8 32.8 1.0
CA B:ASP564 4.8 34.6 1.0
CD B:GLU592 4.8 33.9 1.0

Magnesium binding site 3 out of 4 in 5sgz

Go back to Magnesium Binding Sites List in 5sgz
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.2
occ:1.00
 OD1 C:ASP564 2.0 30.1 1.0
O C:HOH956 2.0 32.5 1.0
O C:HOH994 2.1 31.4 1.0
O C:HOH931 2.1 29.2 1.0
O C:HOH959 2.1 34.7 1.0
O C:HOH917 2.1 31.3 1.0
CG C:ASP564 3.0 31.1 1.0
OD2 C:ASP564 3.4 29.7 1.0
ZN C:ZN801 3.8 35.5 1.0
O C:HOH979 3.9 32.1 1.0
NE2 C:HIS595 4.0 33.8 1.0
CD2 C:HIS563 4.1 28.5 1.0
CD2 C:HIS567 4.2 35.0 1.0
OE2 C:GLU592 4.2 34.5 1.0
O C:HIS563 4.2 32.9 1.0
OG1 C:THR633 4.3 38.4 1.0
CD2 C:HIS595 4.3 32.8 1.0
OD2 C:ASP674 4.3 36.4 1.0
CB C:ASP564 4.3 31.7 1.0
NE2 C:HIS567 4.3 31.5 1.0
O C:HOH987 4.4 41.5 1.0
NE2 C:HIS563 4.6 31.6 1.0
O C:THR633 4.6 32.8 1.0
CA C:ASP564 4.6 33.4 1.0
CB C:THR633 4.6 35.7 1.0
CD2 C:HIS525 4.8 35.6 1.0
CG C:GLU592 4.8 32.9 1.0
NE2 C:HIS525 4.9 33.4 1.0
CD C:GLU592 4.9 36.7 1.0
C C:HIS563 5.0 31.4 1.0

Magnesium binding site 4 out of 4 in 5sgz

Go back to Magnesium Binding Sites List in 5sgz
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.8
occ:1.00
 OD1 D:ASP564 1.9 40.0 1.0
O D:HOH939 2.0 37.7 1.0
O D:HOH914 2.1 42.4 1.0
O D:HOH941 2.1 44.8 1.0
O D:HOH960 2.1 33.5 1.0
O D:HOH913 2.3 37.5 1.0
CG D:ASP564 2.9 35.0 1.0
OD2 D:ASP564 3.3 36.1 1.0
ZN D:ZN801 3.9 43.8 1.0
NE2 D:HIS595 3.9 40.8 1.0
O D:HOH929 4.0 48.3 1.0
OE2 D:GLU592 4.2 49.8 1.0
CD2 D:HIS595 4.2 43.1 1.0
CD2 D:HIS567 4.2 45.7 1.0
OG1 D:THR633 4.2 44.5 1.0
O D:HIS563 4.2 38.6 1.0
CD2 D:HIS563 4.3 34.8 1.0
O D:HOH958 4.3 39.0 1.0
CB D:ASP564 4.3 35.4 1.0
NE2 D:HIS567 4.4 44.1 1.0
OD2 D:ASP674 4.5 40.5 1.0
O D:THR633 4.6 49.0 1.0
CA D:ASP564 4.7 35.6 1.0
CD2 D:HIS525 4.7 48.6 1.0
CB D:THR633 4.7 40.8 1.0
CG D:GLU592 4.7 43.6 1.0
NE2 D:HIS525 4.7 47.5 1.0
NE2 D:HIS563 4.8 34.3 1.0
CD D:GLU592 4.9 45.5 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 03:52:23 2024

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