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Magnesium in PDB 5sk6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sk6 was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.60 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.196, 135.196, 234.886, 90, 90, 120
R / Rfree (%) 18.8 / 23.3

Other elements in 5sk6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide 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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide (pdb code 5sk6). 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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sk6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sk6

Go back to Magnesium Binding Sites List in 5sk6
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.2
occ:1.00
 OD1 A:ASP564 1.9 27.7 1.0
O A:HOH955 2.0 27.4 1.0
O A:HOH988 2.0 27.3 1.0
O A:HOH913 2.1 22.3 1.0
O A:HOH935 2.1 28.4 1.0
O A:HOH943 2.2 27.0 1.0
CG A:ASP564 2.9 30.8 1.0
OD2 A:ASP564 3.3 31.2 1.0
ZN A:ZN801 3.8 36.9 1.0
O A:HOH970 4.0 37.5 1.0
NE2 A:HIS595 4.0 30.1 1.0
OE2 A:GLU592 4.1 35.1 1.0
CD2 A:HIS567 4.2 35.4 1.0
O A:HOH959 4.2 37.3 1.0
CD2 A:HIS563 4.2 31.9 1.0
CB A:ASP564 4.3 29.9 1.0
CD2 A:HIS595 4.3 32.1 1.0
O A:HIS563 4.3 30.7 1.0
OG1 A:THR633 4.3 33.3 1.0
NE2 A:HIS567 4.4 33.7 1.0
CD2 A:HIS525 4.5 32.4 1.0
O A:THR633 4.5 36.1 1.0
OD2 A:ASP674 4.6 41.2 1.0
NE2 A:HIS563 4.6 28.9 1.0
NE2 A:HIS525 4.6 33.0 1.0
CA A:ASP564 4.8 31.4 1.0
CB A:THR633 4.8 33.6 1.0
CG A:GLU592 4.9 32.8 1.0
CD A:GLU592 4.9 36.3 1.0

Magnesium binding site 2 out of 4 in 5sk6

Go back to Magnesium Binding Sites List in 5sk6
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.2
occ:1.00
 O B:HOH950 1.9 28.4 1.0
O B:HOH947 1.9 27.6 1.0
O B:HOH941 2.1 24.9 1.0
O B:HOH921 2.1 24.5 1.0
OD1 B:ASP564 2.1 30.0 1.0
O B:HOH972 2.1 26.3 1.0
CG B:ASP564 3.1 30.5 1.0
OD2 B:ASP564 3.5 32.0 1.0
ZN B:ZN801 3.8 34.1 1.0
O B:HOH960 3.9 40.5 1.0
NE2 B:HIS595 4.0 33.9 1.0
OE2 B:GLU592 4.1 30.6 1.0
O B:HOH1009 4.2 56.7 1.0
OG1 B:THR633 4.2 28.0 1.0
CD2 B:HIS567 4.2 31.8 1.0
CD2 B:HIS563 4.2 29.6 1.0
O B:HOH963 4.2 33.1 1.0
CD2 B:HIS595 4.3 37.6 1.0
O B:HIS563 4.3 37.0 1.0
OD2 B:ASP674 4.3 32.2 1.0
NE2 B:HIS567 4.4 33.0 1.0
CB B:ASP564 4.4 30.1 1.0
O B:THR633 4.5 32.4 1.0
NE2 B:HIS563 4.6 28.2 1.0
CD2 B:HIS525 4.6 34.7 1.0
NE2 B:HIS525 4.7 37.0 1.0
CB B:THR633 4.7 30.4 1.0
CA B:ASP564 4.8 30.5 1.0
CG B:GLU592 4.9 30.5 1.0
CD B:GLU592 4.9 31.4 1.0

Magnesium binding site 3 out of 4 in 5sk6

Go back to Magnesium Binding Sites List in 5sk6
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.4
occ:1.00
 O C:HOH929 2.0 31.4 1.0
OD1 C:ASP564 2.1 27.9 1.0
O C:HOH914 2.1 24.4 1.0
O C:HOH974 2.1 30.8 1.0
O C:HOH999 2.1 30.7 1.0
O C:HOH951 2.2 28.9 1.0
CG C:ASP564 3.0 28.2 1.0
OD2 C:ASP564 3.4 27.9 1.0
ZN C:ZN801 3.7 33.1 1.0
O C:HOH987 4.0 41.2 1.0
NE2 C:HIS595 4.1 32.2 1.0
OG1 C:THR633 4.1 30.2 1.0
OE2 C:GLU592 4.1 31.0 1.0
CD2 C:HIS563 4.2 26.9 1.0
O C:HIS563 4.2 30.5 1.0
CD2 C:HIS567 4.2 31.8 1.0
O C:HOH943 4.3 37.0 1.0
CD2 C:HIS595 4.3 33.6 1.0
OD2 C:ASP674 4.3 30.3 1.0
O C:HOH1009 4.4 51.8 1.0
CB C:ASP564 4.4 26.2 1.0
NE2 C:HIS567 4.4 31.0 1.0
O C:THR633 4.6 32.6 1.0
NE2 C:HIS563 4.6 29.6 1.0
CB C:THR633 4.6 29.8 1.0
CD2 C:HIS525 4.7 37.1 1.0
CA C:ASP564 4.7 28.7 1.0
CG C:GLU592 4.7 30.6 1.0
NE2 C:HIS525 4.8 37.2 1.0
CD C:GLU592 4.9 31.5 1.0
C C:HIS563 5.0 28.0 1.0

Magnesium binding site 4 out of 4 in 5sk6

Go back to Magnesium Binding Sites List in 5sk6
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide


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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:49.1
occ:1.00
 O D:HOH931 1.9 43.9 1.0
O D:HOH935 2.0 42.4 1.0
O D:HOH916 2.1 40.3 1.0
OD1 D:ASP564 2.1 47.4 1.0
O D:HOH932 2.2 36.3 1.0
O D:HOH912 2.3 41.3 1.0
CG D:ASP564 3.1 45.5 1.0
OD2 D:ASP564 3.4 49.0 1.0
O D:HOH945 3.6 44.9 1.0
O D:HOH944 3.8 45.7 1.0
ZN D:ZN801 3.9 52.8 1.0
OE2 D:GLU592 3.9 48.7 1.0
CD2 D:HIS567 4.0 47.7 1.0
NE2 D:HIS595 4.0 54.4 1.0
NE2 D:HIS567 4.1 47.2 1.0
CD2 D:HIS595 4.4 51.6 1.0
CD2 D:HIS525 4.5 58.5 1.0
CB D:ASP564 4.5 46.7 1.0
NE2 D:HIS525 4.5 58.9 1.0
OG1 D:THR633 4.5 47.7 1.0
O D:HIS563 4.6 44.9 1.0
CD2 D:HIS563 4.6 40.9 1.0
OD2 D:ASP674 4.7 50.0 1.0
O D:THR633 4.7 52.7 1.0
CA D:ASP564 4.9 44.3 1.0
CD D:GLU592 4.9 49.3 1.0
NE2 D:HIS563 5.0 39.9 1.0
CB D:THR633 5.0 49.3 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 04:30:40 2024

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