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Magnesium in PDB 5sip: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-N-(2-Phenylimidazo[1,2-A]Pyrimidin-7- Yl)Pyrazole-3-Carboxamide, PDB code: 5sip 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) 43.72 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.361, 135.361, 235.604, 90, 90, 120
R / Rfree (%) 19.1 / 22.7

Other elements in 5sip:

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

Magnesium binding site 1 out of 4 in 5sip

Go back to Magnesium Binding Sites List in 5sip
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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:26.3
occ:1.00
 O A:HOH1001 1.9 24.4 1.0
OD1 A:ASP564 2.0 24.8 1.0
O A:HOH928 2.0 27.7 1.0
O A:HOH927 2.0 20.9 1.0
O A:HOH952 2.1 25.4 1.0
O A:HOH934 2.2 27.4 1.0
CG A:ASP564 3.0 27.4 1.0
OD2 A:ASP564 3.4 29.7 1.0
ZN A:ZN801 3.8 33.1 1.0
O A:HOH979 4.0 39.4 1.0
OE2 A:GLU592 4.0 34.8 1.0
O A:HOH1011 4.1 56.3 1.0
NE2 A:HIS595 4.1 32.5 1.0
CD2 A:HIS567 4.2 32.2 1.0
O A:HOH990 4.3 37.7 1.0
CD2 A:HIS563 4.3 25.6 1.0
OG1 A:THR633 4.3 33.6 1.0
CD2 A:HIS595 4.3 30.8 1.0
CB A:ASP564 4.4 26.8 1.0
O A:HIS563 4.4 30.1 1.0
OD2 A:ASP674 4.4 41.4 1.0
NE2 A:HIS567 4.4 30.8 1.0
O A:THR633 4.5 31.7 1.0
NE2 A:HIS563 4.6 26.4 1.0
CD2 A:HIS525 4.7 32.0 1.0
NE2 A:HIS525 4.7 34.3 1.0
CB A:THR633 4.7 32.2 1.0
CA A:ASP564 4.8 27.5 1.0
CG A:GLU592 4.9 31.7 1.0
CD A:GLU592 4.9 33.0 1.0

Magnesium binding site 2 out of 4 in 5sip

Go back to Magnesium Binding Sites List in 5sip
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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:23.4
occ:1.00
 O B:HOH922 1.9 22.9 1.0
O B:HOH917 2.0 20.6 1.0
O B:HOH998 2.1 23.8 1.0
OD1 B:ASP564 2.1 27.6 1.0
O B:HOH924 2.1 20.7 1.0
O B:HOH981 2.1 23.0 1.0
CG B:ASP564 3.1 26.4 1.0
OD2 B:ASP564 3.4 26.4 1.0
ZN B:ZN801 3.8 32.3 1.0
O B:HOH978 4.0 33.8 1.0
OE2 B:GLU592 4.0 30.8 1.0
NE2 B:HIS595 4.1 29.1 1.0
CD2 B:HIS563 4.2 24.6 1.0
OG1 B:THR633 4.2 26.4 1.0
CD2 B:HIS567 4.3 27.5 1.0
O B:HOH966 4.3 36.9 1.0
OD2 B:ASP674 4.3 28.6 1.0
O B:HIS563 4.3 29.4 1.0
CD2 B:HIS595 4.4 30.3 1.0
NE2 B:HIS567 4.4 28.3 1.0
CB B:ASP564 4.4 25.7 1.0
O B:THR633 4.5 26.5 1.0
NE2 B:HIS563 4.6 24.3 1.0
CD2 B:HIS525 4.6 28.5 1.0
NE2 B:HIS525 4.7 30.2 1.0
CB B:THR633 4.7 29.2 1.0
CG B:GLU592 4.8 29.4 1.0
CA B:ASP564 4.8 25.8 1.0
CD B:GLU592 4.9 29.3 1.0

Magnesium binding site 3 out of 4 in 5sip

Go back to Magnesium Binding Sites List in 5sip
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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:29.2
occ:1.00
 O C:HOH959 2.0 28.9 1.0
O C:HOH969 2.0 27.2 1.0
O C:HOH999 2.1 25.6 1.0
O C:HOH933 2.1 28.2 1.0
OD1 C:ASP564 2.1 28.5 1.0
O C:HOH931 2.1 24.1 1.0
CG C:ASP564 3.2 28.9 1.0
OD2 C:ASP564 3.5 28.3 1.0
ZN C:ZN801 3.8 35.0 1.0
NE2 C:HIS595 4.0 29.5 1.0
OE2 C:GLU592 4.0 33.0 1.0
O C:HOH991 4.1 40.4 1.0
CD2 C:HIS567 4.2 31.7 1.0
OG1 C:THR633 4.3 29.6 1.0
O C:HOH986 4.3 33.9 1.0
NE2 C:HIS567 4.3 31.1 1.0
CD2 C:HIS563 4.3 27.8 1.0
CD2 C:HIS595 4.3 29.2 1.0
O C:HIS563 4.3 30.5 1.0
OD2 C:ASP674 4.4 34.7 1.0
O C:THR633 4.4 30.7 1.0
CB C:ASP564 4.5 27.4 1.0
CD2 C:HIS525 4.7 37.5 1.0
NE2 C:HIS525 4.7 37.9 1.0
CB C:THR633 4.7 30.2 1.0
NE2 C:HIS563 4.8 30.2 1.0
CG C:GLU592 4.8 30.3 1.0
CA C:ASP564 4.8 27.3 1.0
CD C:GLU592 4.9 32.2 1.0

Magnesium binding site 4 out of 4 in 5sip

Go back to Magnesium Binding Sites List in 5sip
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-2-Methyl-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- (Azetidine-1-Carbonyl)-2-Methyl-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:38.9
occ:1.00
 O D:HOH914 2.1 30.7 1.0
O D:HOH960 2.1 31.3 1.0
O D:HOH958 2.1 32.1 1.0
O D:HOH906 2.1 32.1 1.0
O D:HOH915 2.1 36.4 1.0
OD1 D:ASP564 2.2 33.4 1.0
CG D:ASP564 3.2 32.9 1.0
OD2 D:ASP564 3.6 38.8 1.0
ZN D:ZN801 3.8 40.6 1.0
O D:HOH959 3.9 39.8 1.0
OE2 D:GLU592 4.0 37.8 1.0
O D:HOH967 4.1 39.8 1.0
NE2 D:HIS595 4.1 39.5 1.0
OG1 D:THR633 4.2 34.7 1.0
CD2 D:HIS567 4.3 41.9 1.0
OD2 D:ASP674 4.4 41.0 1.0
CD2 D:HIS595 4.4 39.0 1.0
NE2 D:HIS567 4.4 38.5 1.0
CD2 D:HIS563 4.4 31.5 1.0
O D:HIS563 4.4 32.5 1.0
O D:THR633 4.5 38.4 1.0
CB D:ASP564 4.5 35.6 1.0
CD2 D:HIS525 4.6 39.3 1.0
NE2 D:HIS525 4.7 43.0 1.0
CB D:THR633 4.7 35.7 1.0
O D:HOH971 4.8 47.2 1.0
CD D:GLU592 4.8 39.4 1.0
CA D:ASP564 4.9 32.6 1.0
CG D:GLU592 4.9 40.5 1.0
NE2 D:HIS563 4.9 30.8 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 04:13:43 2024

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