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Magnesium in PDB 5sh6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One, PDB code: 5sh6 was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.44 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.064, 135.064, 233.963, 90, 90, 120
R / Rfree (%) 17.5 / 21.7

Other elements in 5sh6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One 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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One (pdb code 5sh6). 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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One, PDB code: 5sh6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh6

Go back to Magnesium Binding Sites List in 5sh6
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.2
occ:1.00
 O A:HOH1028 2.0 24.7 1.0
O A:HOH962 2.0 23.4 1.0
O A:HOH936 2.0 22.5 1.0
OD1 A:ASP564 2.0 26.1 1.0
O A:HOH968 2.1 24.0 1.0
O A:HOH925 2.1 24.6 1.0
CG A:ASP564 3.0 27.2 1.0
OD2 A:ASP564 3.4 27.9 1.0
ZN A:ZN801 3.7 31.2 1.0
OE2 A:GLU592 4.0 31.3 1.0
O A:HOH1013 4.0 33.0 1.0
NE2 A:HIS595 4.0 26.9 1.0
OG1 A:THR633 4.2 26.8 1.0
O A:HOH997 4.2 27.9 1.0
CD2 A:HIS563 4.3 23.9 1.0
CD2 A:HIS567 4.3 26.8 1.0
O A:HIS563 4.3 29.5 1.0
CD2 A:HIS595 4.3 24.9 1.0
CB A:ASP564 4.4 26.9 1.0
OD2 A:ASP674 4.5 33.1 1.0
O A:THR633 4.5 29.0 1.0
NE2 A:HIS567 4.5 26.3 1.0
CD2 A:HIS525 4.6 29.4 1.0
CB A:THR633 4.6 26.3 1.0
NE2 A:HIS563 4.6 27.1 1.0
NE2 A:HIS525 4.7 31.2 1.0
CG A:GLU592 4.7 26.4 1.0
CA A:ASP564 4.8 29.2 1.0
CD A:GLU592 4.8 28.8 1.0

Magnesium binding site 2 out of 4 in 5sh6

Go back to Magnesium Binding Sites List in 5sh6
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.1
occ:1.00
 O B:HOH958 2.0 22.1 1.0
O B:HOH951 2.0 25.6 1.0
O B:HOH1006 2.1 20.7 1.0
O B:HOH1021 2.1 24.4 1.0
OD1 B:ASP564 2.1 25.4 1.0
O B:HOH917 2.1 21.8 1.0
CG B:ASP564 3.0 25.3 1.0
OD2 B:ASP564 3.4 27.2 1.0
ZN B:ZN801 3.7 31.0 1.0
O B:HOH1038 3.8 51.1 1.0
O B:HOH973 4.0 40.4 1.0
OE2 B:GLU592 4.0 28.3 1.0
NE2 B:HIS595 4.0 26.0 1.0
OG1 B:THR633 4.1 25.5 1.0
CD2 B:HIS563 4.2 24.2 1.0
O B:HOH984 4.3 26.9 1.0
CD2 B:HIS567 4.3 30.1 1.0
O B:HIS563 4.3 26.1 1.0
CD2 B:HIS595 4.3 27.4 1.0
OD2 B:ASP674 4.4 26.8 1.0
CB B:ASP564 4.4 22.5 1.0
NE2 B:HIS567 4.5 26.4 1.0
O B:THR633 4.5 24.8 1.0
NE2 B:HIS563 4.6 24.5 1.0
CB B:THR633 4.6 26.6 1.0
CD2 B:HIS525 4.6 28.9 1.0
NE2 B:HIS525 4.7 30.8 1.0
CA B:ASP564 4.7 23.5 1.0
CG B:GLU592 4.7 26.2 1.0
CD B:GLU592 4.8 26.8 1.0

Magnesium binding site 3 out of 4 in 5sh6

Go back to Magnesium Binding Sites List in 5sh6
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:27.1
occ:1.00
 O C:HOH979 2.0 23.4 1.0
OD1 C:ASP564 2.0 23.5 1.0
O C:HOH934 2.0 26.4 1.0
O C:HOH1039 2.1 28.7 1.0
O C:HOH1007 2.1 25.5 1.0
O C:HOH939 2.2 23.8 1.0
CG C:ASP564 3.1 26.1 1.0
OD2 C:ASP564 3.4 25.9 1.0
ZN C:ZN801 3.7 32.0 1.0
O C:HOH1049 3.8 46.1 1.0
O C:HOH1004 3.9 36.8 1.0
OE2 C:GLU592 4.0 30.9 1.0
OG1 C:THR633 4.1 25.3 1.0
NE2 C:HIS595 4.1 26.7 1.0
CD2 C:HIS563 4.2 26.1 1.0
CD2 C:HIS567 4.3 28.3 1.0
O C:HOH1013 4.3 30.1 1.0
O C:HIS563 4.3 26.7 1.0
CD2 C:HIS595 4.4 26.2 1.0
OD2 C:ASP674 4.4 32.6 1.0
CB C:ASP564 4.4 23.4 1.0
O C:THR633 4.5 27.2 1.0
NE2 C:HIS567 4.5 28.6 1.0
NE2 C:HIS563 4.6 28.5 1.0
CB C:THR633 4.6 26.8 1.0
CD2 C:HIS525 4.7 29.5 1.0
CA C:ASP564 4.7 26.5 1.0
NE2 C:HIS525 4.8 30.5 1.0
CD C:GLU592 4.8 30.4 1.0
CG C:GLU592 4.8 27.8 1.0

Magnesium binding site 4 out of 4 in 5sh6

Go back to Magnesium Binding Sites List in 5sh6
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-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 4-[2- (1-Methylbenzimidazol-2-Yl)Ethyl]-2,3-Dihydro-1,4-Benzoxazepin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:32.6
occ:1.00
 O D:HOH955 2.0 26.8 1.0
O D:HOH974 2.1 25.9 1.0
O D:HOH906 2.1 26.9 1.0
O D:HOH934 2.1 28.6 1.0
OD1 D:ASP564 2.1 29.7 1.0
O D:HOH960 2.2 31.9 1.0
CG D:ASP564 3.1 30.2 1.0
OD2 D:ASP564 3.4 33.2 1.0
ZN D:ZN801 3.7 35.5 1.0
O D:HOH950 3.9 34.2 1.0
OE2 D:GLU592 4.0 33.0 1.0
NE2 D:HIS595 4.1 32.6 1.0
O D:HOH961 4.1 36.0 1.0
OG1 D:THR633 4.1 31.4 1.0
CD2 D:HIS563 4.3 28.1 1.0
CD2 D:HIS567 4.3 35.0 1.0
CD2 D:HIS595 4.3 29.6 1.0
O D:HIS563 4.3 31.3 1.0
OD2 D:ASP674 4.4 36.0 1.0
O D:THR633 4.4 34.5 1.0
CB D:ASP564 4.5 31.4 1.0
CD2 D:HIS525 4.5 34.4 1.0
NE2 D:HIS525 4.6 40.1 1.0
NE2 D:HIS567 4.6 32.8 1.0
CB D:THR633 4.6 32.3 1.0
NE2 D:HIS563 4.7 26.7 1.0
CA D:ASP564 4.9 30.3 1.0
CG D:GLU592 4.9 37.2 1.0
CD D:GLU592 4.9 35.7 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 03:54:37 2024

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