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Magnesium in PDB 5sjp: Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate, PDB code: 5sjp was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.25
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.3, 135.3, 234.703, 90, 90, 120
R / Rfree (%) 17.3 / 23.4

Other elements in 5sjp:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate 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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate (pdb code 5sjp). 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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate, PDB code: 5sjp:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjp

Go back to Magnesium Binding Sites List in 5sjp
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:31.4
occ:1.00
 O A:HOH986 1.9 32.6 1.0
OD1 A:ASP564 1.9 30.3 1.0
O A:HOH960 2.0 29.7 1.0
O A:HOH919 2.0 26.2 1.0
O A:HOH948 2.2 27.2 1.0
O A:HOH946 2.2 30.8 1.0
CG A:ASP564 2.8 33.1 1.0
OD2 A:ASP564 3.1 37.3 1.0
ZN A:ZN801 3.6 38.8 1.0
O A:HOH957 3.8 38.6 1.0
NE2 A:HIS595 4.0 29.2 1.0
O A:HOH939 4.1 40.3 1.0
OE2 A:GLU592 4.1 36.3 1.0
CD2 A:HIS567 4.2 33.2 1.0
O A:HOH988 4.2 56.4 1.0
CB A:ASP564 4.2 30.1 1.0
CD2 A:HIS563 4.3 26.9 1.0
NE2 A:HIS567 4.3 34.2 1.0
O A:HIS563 4.4 32.8 1.0
CD2 A:HIS595 4.4 32.3 1.0
CD2 A:HIS525 4.4 35.1 1.0
OG1 A:THR633 4.5 33.5 1.0
NE2 A:HIS525 4.5 34.6 1.0
NE2 A:HIS563 4.5 25.6 1.0
CA A:ASP564 4.7 31.6 1.0
O A:THR633 4.7 36.8 1.0
OD2 A:ASP674 4.7 41.9 1.0
CB A:THR633 4.8 32.7 1.0
CD A:GLU592 5.0 34.6 1.0
CG A:GLU592 5.0 32.9 1.0

Magnesium binding site 2 out of 4 in 5sjp

Go back to Magnesium Binding Sites List in 5sjp
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.5
occ:1.00
 O B:HOH925 1.9 32.1 1.0
O B:HOH942 2.0 27.1 1.0
O B:HOH972 2.1 25.4 1.0
O B:HOH910 2.1 25.8 1.0
O B:HOH984 2.1 26.6 1.0
OD1 B:ASP564 2.1 33.9 1.0
CG B:ASP564 3.1 27.4 1.0
OD2 B:ASP564 3.3 32.4 1.0
ZN B:ZN801 3.7 38.5 1.0
O B:HOH940 3.9 41.0 1.0
OE2 B:GLU592 4.1 32.7 1.0
O B:HOH959 4.1 40.7 1.0
O B:HOH1002 4.1 53.0 1.0
NE2 B:HIS595 4.1 35.4 1.0
CD2 B:HIS563 4.1 32.6 1.0
OG1 B:THR633 4.2 33.5 1.0
CD2 B:HIS567 4.3 33.8 1.0
NE2 B:HIS567 4.3 33.4 1.0
O B:HIS563 4.4 35.5 1.0
OD2 B:ASP674 4.4 34.2 1.0
CD2 B:HIS595 4.4 41.2 1.0
CB B:ASP564 4.4 27.2 1.0
O B:THR633 4.5 34.6 1.0
NE2 B:HIS563 4.5 31.8 1.0
CB B:THR633 4.6 32.1 1.0
CD2 B:HIS525 4.7 34.8 1.0
NE2 B:HIS525 4.7 37.8 1.0
CG B:GLU592 4.8 31.9 1.0
CA B:ASP564 4.8 34.9 1.0
CD B:GLU592 4.9 31.9 1.0

Magnesium binding site 3 out of 4 in 5sjp

Go back to Magnesium Binding Sites List in 5sjp
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.6
occ:1.00
 O C:HOH957 2.0 34.5 1.0
O C:HOH964 2.0 25.7 1.0
OD1 C:ASP564 2.0 33.3 1.0
O C:HOH939 2.1 30.9 1.0
O C:HOH987 2.1 34.5 1.0
O C:HOH935 2.1 32.8 1.0
CG C:ASP564 3.1 34.2 1.0
OD2 C:ASP564 3.4 35.7 1.0
ZN C:ZN801 3.7 40.1 1.0
O C:HOH1005 3.9 44.9 1.0
OE2 C:GLU592 4.0 34.3 1.0
O C:HOH938 4.0 36.6 1.0
O C:HOH961 4.2 35.8 1.0
NE2 C:HIS595 4.2 37.4 1.0
OG1 C:THR633 4.2 32.6 1.0
CD2 C:HIS563 4.2 27.6 1.0
CD2 C:HIS567 4.2 35.5 1.0
O C:HIS563 4.4 30.0 1.0
NE2 C:HIS567 4.4 39.7 1.0
CB C:ASP564 4.4 30.6 1.0
OD2 C:ASP674 4.5 35.9 1.0
O C:THR633 4.5 34.1 1.0
CD2 C:HIS595 4.5 34.4 1.0
NE2 C:HIS525 4.6 35.8 1.0
NE2 C:HIS563 4.6 33.1 1.0
CD2 C:HIS525 4.6 40.2 1.0
CB C:THR633 4.7 31.7 1.0
CG C:GLU592 4.8 31.9 1.0
CD C:GLU592 4.8 35.6 1.0
CA C:ASP564 4.8 33.6 1.0
O C:HOH1009 4.9 41.9 1.0

Magnesium binding site 4 out of 4 in 5sjp

Go back to Magnesium Binding Sites List in 5sjp
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate


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 Ethyl N-[[4-[[4-(Azetidine-1-Carbonyl)-2-Methylpyrazole-3-Carbonyl]Amino]- 6-Methylpyridin-2-Yl]Carbamothioyl]Carbamate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:44.4
occ:1.00
 O D:HOH926 2.0 33.8 1.0
O D:HOH937 2.1 40.7 1.0
O D:HOH907 2.1 43.3 1.0
O D:HOH939 2.2 41.3 1.0
OD1 D:ASP564 2.2 46.6 1.0
O D:HOH905 2.4 40.8 1.0
CG D:ASP564 3.1 47.7 1.0
OD2 D:ASP564 3.3 48.2 1.0
O D:HOH911 3.8 49.1 1.0
ZN D:ZN801 3.8 52.3 1.0
OE2 D:GLU592 3.9 51.4 1.0
NE2 D:HIS595 4.2 53.0 1.0
CD2 D:HIS567 4.2 54.3 1.0
CD2 D:HIS563 4.3 47.7 1.0
OG1 D:THR633 4.3 43.8 1.0
NE2 D:HIS567 4.4 48.8 1.0
CD2 D:HIS595 4.4 50.2 1.0
O D:HIS563 4.4 53.4 1.0
CB D:ASP564 4.5 46.3 1.0
O D:THR633 4.5 47.6 1.0
OD2 D:ASP674 4.6 46.4 1.0
NE2 D:HIS525 4.6 59.7 1.0
CD2 D:HIS525 4.6 54.3 1.0
NE2 D:HIS563 4.6 38.0 1.0
CB D:THR633 4.7 44.4 1.0
CD D:GLU592 4.8 47.6 1.0
CA D:ASP564 4.8 48.1 1.0
CG D:GLU592 4.9 51.8 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: Mon Sep 30 04:24:16 2024

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