Atomistry » Magnesium » PDB 5sja-5skd » 5sjy
Atomistry »
  Magnesium »
    PDB 5sja-5skd »
      5sjy »

Magnesium in PDB 5sjy: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy 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) 43.81 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.053, 136.053, 235.986, 90, 90, 120
R / Rfree (%) 20.2 / 26.5

Other elements in 5sjy:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide also contains other interesting chemical elements:

Zinc (Zn) 4 atoms
Bromine (Br) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide (pdb code 5sjy). 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjy:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:32.8
occ:1.00
 O A:HOH934 1.8 33.2 1.0
O A:HOH908 1.9 34.0 1.0
OD1 A:ASP564 1.9 34.2 1.0
O A:HOH909 2.0 34.2 1.0
O A:HOH918 2.2 33.7 1.0
O A:HOH931 2.2 30.9 1.0
CG A:ASP564 2.9 34.3 1.0
OD2 A:ASP564 3.3 41.0 1.0
ZN A:ZN801 3.7 42.2 1.0
O A:HOH929 3.8 45.5 1.0
NE2 A:HIS595 4.0 30.2 1.0
OE2 A:GLU592 4.0 44.3 1.0
O A:HIS563 4.1 35.5 1.0
O A:HOH920 4.1 44.0 1.0
CD2 A:HIS563 4.1 40.7 1.0
OG1 A:THR633 4.2 41.0 1.0
CB A:ASP564 4.3 33.0 1.0
CD2 A:HIS595 4.3 37.2 1.0
CD2 A:HIS567 4.4 41.5 1.0
OD2 A:ASP674 4.4 38.9 1.0
O A:THR633 4.5 39.4 1.0
NE2 A:HIS567 4.5 36.1 1.0
CD2 A:HIS525 4.6 45.9 1.0
CB A:THR633 4.6 35.4 1.0
NE2 A:HIS563 4.6 37.9 1.0
NE2 A:HIS525 4.7 40.9 1.0
CA A:ASP564 4.7 33.0 1.0
CG A:GLU592 4.8 37.7 1.0
CD A:GLU592 4.9 43.2 1.0
C A:HIS563 4.9 34.5 1.0

Magnesium binding site 2 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.4
occ:1.00
 OD1 B:ASP564 2.0 36.8 1.0
O B:HOH924 2.0 28.7 1.0
O B:HOH933 2.1 32.6 1.0
O B:HOH929 2.2 29.9 1.0
O B:HOH945 2.2 34.4 1.0
O B:HOH909 2.3 31.5 1.0
CG B:ASP564 2.9 31.8 1.0
OD2 B:ASP564 3.2 30.5 1.0
ZN B:ZN801 3.7 39.3 1.0
O B:HOH947 4.0 42.9 1.0
OE2 B:GLU592 4.2 35.5 1.0
NE2 B:HIS595 4.2 36.8 1.0
CD2 B:HIS563 4.2 33.7 1.0
O B:HOH932 4.2 47.8 1.0
CD2 B:HIS567 4.3 39.5 1.0
O B:HIS563 4.3 42.5 1.0
CB B:ASP564 4.3 29.5 1.0
OG1 B:THR633 4.3 33.1 1.0
CD2 B:HIS595 4.4 38.4 1.0
OD2 B:ASP674 4.4 35.8 1.0
NE2 B:HIS563 4.5 30.1 1.0
NE2 B:HIS567 4.5 37.1 1.0
CD2 B:HIS525 4.5 36.1 1.0
O B:THR633 4.5 35.8 1.0
NE2 B:HIS525 4.6 39.8 1.0
CA B:ASP564 4.7 33.1 1.0
CB B:THR633 4.7 34.9 1.0
CG B:GLU592 5.0 41.3 1.0
CD B:GLU592 5.0 40.3 1.0

Magnesium binding site 3 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:33.6
occ:1.00
 O C:HOH937 1.9 39.9 1.0
O C:HOH939 2.0 29.6 1.0
OD1 C:ASP564 2.1 30.5 1.0
O C:HOH930 2.1 36.8 1.0
O C:HOH956 2.2 29.6 1.0
O C:HOH924 2.2 30.2 1.0
CG C:ASP564 3.1 33.8 1.0
OD2 C:ASP564 3.6 33.1 1.0
OE2 C:GLU592 3.9 37.8 1.0
ZN C:ZN801 3.9 38.5 1.0
NE2 C:HIS595 4.0 50.9 1.0
O C:HOH940 4.1 35.3 1.0
O C:HOH945 4.2 48.8 1.0
CD2 C:HIS567 4.2 32.0 1.0
O C:HIS563 4.3 37.4 1.0
CD2 C:HIS595 4.3 43.7 1.0
CD2 C:HIS563 4.3 32.5 1.0
OG1 C:THR633 4.3 40.8 1.0
NE2 C:HIS567 4.4 37.4 1.0
CB C:ASP564 4.4 30.4 1.0
OD2 C:ASP674 4.5 39.6 1.0
O C:THR633 4.6 36.6 1.0
CG C:GLU592 4.7 38.7 1.0
CB C:THR633 4.7 39.5 1.0
CD C:GLU592 4.7 40.5 1.0
CA C:ASP564 4.8 34.0 1.0
NE2 C:HIS563 4.8 38.8 1.0
CD2 C:HIS525 4.8 40.6 1.0
NE2 C:HIS525 4.8 47.9 1.0
CE1 C:HIS595 5.0 43.7 1.0

Magnesium binding site 4 out of 4 in 5sjy

Go back to Magnesium Binding Sites List in 5sjy
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 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- Bromo-2,5-Dimethyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:47.7
occ:1.00
 O D:HOH917 2.0 41.4 1.0
O D:HOH909 2.0 37.1 1.0
O D:HOH902 2.1 45.9 1.0
O D:HOH907 2.1 31.2 1.0
OD1 D:ASP564 2.2 47.7 1.0
O D:HOH915 2.3 37.5 1.0
CG D:ASP564 3.1 42.2 1.0
OD2 D:ASP564 3.4 48.6 1.0
ZN D:ZN801 3.9 46.8 1.0
O D:HOH913 4.0 41.5 1.0
OE2 D:GLU592 4.1 49.4 1.0
NE2 D:HIS595 4.1 43.8 1.0
OG1 D:THR633 4.1 42.1 1.0
O D:THR633 4.3 55.3 1.0
CD2 D:HIS567 4.4 54.4 1.0
CD2 D:HIS563 4.4 39.0 1.0
OD2 D:ASP674 4.4 35.1 1.0
CB D:ASP564 4.4 43.0 1.0
CD2 D:HIS595 4.5 44.8 1.0
O D:HIS563 4.5 38.1 1.0
NE2 D:HIS567 4.5 49.2 1.0
CD2 D:HIS525 4.5 51.6 1.0
CB D:THR633 4.6 45.3 1.0
NE2 D:HIS525 4.6 47.6 1.0
NE2 D:HIS563 4.8 38.6 1.0
CG D:GLU592 4.9 47.3 1.0
CA D:ASP564 4.9 40.7 1.0
CD D:GLU592 4.9 46.9 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 04:27:49 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy