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Magnesium in PDB 5si8: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide, PDB code: 5si8 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) 33.88 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.16, 135.16, 234.727, 90, 90, 120
R / Rfree (%) 19.6 / 24.6

Other elements in 5si8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide (pdb code 5si8). 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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide, PDB code: 5si8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5si8

Go back to Magnesium Binding Sites List in 5si8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.0
occ:1.00
 O A:HOH908 1.8 27.9 1.0
O A:HOH980 1.9 31.0 1.0
O A:HOH953 1.9 25.3 1.0
OD1 A:ASP564 2.1 27.7 1.0
O A:HOH931 2.1 34.1 1.0
O A:HOH916 2.3 32.2 1.0
CG A:ASP564 3.0 31.3 1.0
OD2 A:ASP564 3.3 32.6 1.0
O A:HOH983 3.8 33.4 1.0
ZN A:ZN801 3.8 35.0 1.0
O A:HOH987 3.9 52.5 1.0
NE2 A:HIS595 4.0 32.4 1.0
OE2 A:GLU592 4.1 36.2 1.0
O A:HOH939 4.1 40.1 1.0
CD2 A:HIS567 4.1 34.7 1.0
CD2 A:HIS595 4.3 31.1 1.0
CD2 A:HIS563 4.3 29.6 1.0
NE2 A:HIS567 4.4 35.3 1.0
O A:HIS563 4.4 34.0 1.0
CB A:ASP564 4.4 30.6 1.0
OG1 A:THR633 4.5 44.2 1.0
CD2 A:HIS525 4.5 32.0 1.0
OD2 A:ASP674 4.5 38.8 1.0
NE2 A:HIS525 4.5 30.8 1.0
O A:THR633 4.6 36.9 1.0
NE2 A:HIS563 4.6 33.5 1.0
CA A:ASP564 4.8 32.3 1.0
O A:HOH994 4.8 39.4 1.0
CB A:THR633 4.8 40.4 1.0
CD A:GLU592 4.9 36.7 1.0
CG A:GLU592 4.9 35.4 1.0

Magnesium binding site 2 out of 4 in 5si8

Go back to Magnesium Binding Sites List in 5si8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.2
occ:1.00
 O B:HOH951 1.8 28.2 1.0
O B:HOH938 2.0 24.8 1.0
OD1 B:ASP564 2.0 30.1 1.0
O B:HOH901 2.1 24.2 1.0
O B:HOH955 2.1 23.7 1.0
O B:HOH954 2.2 25.4 1.0
CG B:ASP564 3.0 28.3 1.0
OD2 B:ASP564 3.3 29.8 1.0
ZN B:ZN801 3.7 34.4 1.0
O B:HOH1003 3.9 41.5 1.0
OE2 B:GLU592 4.0 27.6 1.0
O B:HOH945 4.1 35.8 1.0
NE2 B:HIS595 4.1 28.9 1.0
CD2 B:HIS563 4.1 26.6 1.0
O B:HOH969 4.2 36.3 1.0
O B:HIS563 4.2 32.4 1.0
OG1 B:THR633 4.3 28.6 1.0
CD2 B:HIS567 4.3 31.7 1.0
OD2 B:ASP674 4.3 33.1 1.0
CB B:ASP564 4.4 29.3 1.0
CD2 B:HIS595 4.4 27.8 1.0
NE2 B:HIS563 4.4 26.3 1.0
NE2 B:HIS567 4.4 31.7 1.0
CD2 B:HIS525 4.5 31.8 1.0
O B:THR633 4.6 34.9 1.0
CB B:THR633 4.6 29.8 1.0
NE2 B:HIS525 4.6 36.5 1.0
CA B:ASP564 4.7 30.2 1.0
CG B:GLU592 4.8 30.4 1.0
CD B:GLU592 4.8 31.7 1.0
OD1 B:ASP674 5.0 32.0 1.0

Magnesium binding site 3 out of 4 in 5si8

Go back to Magnesium Binding Sites List in 5si8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:28.0
occ:1.00
 O C:HOH946 2.0 23.6 1.0
O C:HOH935 2.0 26.2 1.0
O C:HOH977 2.1 26.4 1.0
OD1 C:ASP564 2.1 31.2 1.0
O C:HOH931 2.1 30.4 1.0
O C:HOH992 2.2 29.2 1.0
CG C:ASP564 3.1 29.2 1.0
OD2 C:ASP564 3.4 28.8 1.0
ZN C:ZN801 3.8 33.9 1.0
O C:HOH984 4.0 39.5 1.0
OE2 C:GLU592 4.0 35.4 1.0
O C:HOH950 4.1 34.9 1.0
OG1 C:THR633 4.1 32.1 1.0
CD2 C:HIS563 4.1 25.3 1.0
NE2 C:HIS595 4.1 30.9 1.0
CD2 C:HIS567 4.2 30.5 1.0
O C:HIS563 4.4 30.9 1.0
CD2 C:HIS595 4.4 30.4 1.0
OD2 C:ASP674 4.4 32.6 1.0
NE2 C:HIS563 4.4 28.9 1.0
CB C:ASP564 4.5 28.1 1.0
O C:THR633 4.5 33.2 1.0
NE2 C:HIS567 4.5 33.4 1.0
CB C:THR633 4.6 28.7 1.0
CG C:GLU592 4.8 33.2 1.0
CA C:ASP564 4.8 29.7 1.0
CD C:GLU592 4.8 33.0 1.0
CD2 C:HIS525 4.9 33.3 1.0
NE2 C:HIS525 5.0 35.2 1.0

Magnesium binding site 4 out of 4 in 5si8

Go back to Magnesium Binding Sites List in 5si8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-1-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:41.1
occ:1.00
 O D:HOH912 1.8 32.8 1.0
O D:HOH960 1.9 41.6 1.0
OD1 D:ASP564 2.1 35.4 1.0
O D:HOH911 2.1 28.5 1.0
O D:HOH919 2.4 38.4 1.0
O D:HOH907 2.4 31.8 1.0
CG D:ASP564 3.0 36.1 1.0
OD2 D:ASP564 3.2 36.4 1.0
ZN D:ZN801 3.8 43.5 1.0
O D:HOH953 3.8 38.7 1.0
OE2 D:GLU592 4.0 46.6 1.0
CD2 D:HIS567 4.2 41.9 1.0
NE2 D:HIS525 4.3 45.3 1.0
CD2 D:HIS525 4.3 43.2 1.0
NE2 D:HIS567 4.4 41.0 1.0
NE2 D:HIS595 4.4 45.9 1.0
OD2 D:ASP674 4.4 44.9 1.0
CB D:ASP564 4.4 37.5 1.0
OG1 D:THR633 4.4 38.7 1.0
CD2 D:HIS563 4.5 39.1 1.0
O D:THR633 4.5 44.0 1.0
CD2 D:HIS595 4.6 42.5 1.0
O D:HIS563 4.7 40.7 1.0
NE2 D:HIS563 4.7 40.7 1.0
CB D:THR633 4.9 42.6 1.0
CA D:ASP564 4.9 37.5 1.0
CD D:GLU592 4.9 46.2 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 04:08:05 2024

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