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Magnesium in PDB 5sjl: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sjl was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.76 / 2.64
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.938, 135.938, 235.673, 90, 90, 120
R / Rfree (%) 20.2 / 24.4

Other elements in 5sjl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide (pdb code 5sjl). 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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide, PDB code: 5sjl:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjl

Go back to Magnesium Binding Sites List in 5sjl
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:29.0
occ:1.00
 O A:HOH926 1.7 28.4 1.0
O A:HOH969 2.0 31.5 1.0
O A:HOH908 2.1 29.5 1.0
O A:HOH948 2.1 24.3 1.0
OD1 A:ASP564 2.1 35.7 1.0
CG A:ASP564 3.2 36.7 1.0
OD2 A:ASP564 3.5 40.1 1.0
OE2 A:GLU592 3.7 31.8 1.0
ZN A:ZN801 3.9 38.0 1.0
NE2 A:HIS595 4.0 34.8 1.0
CD2 A:HIS595 4.2 33.3 1.0
CD2 A:HIS563 4.3 31.8 1.0
O A:HIS563 4.3 29.8 1.0
CD2 A:HIS567 4.3 35.1 1.0
OG1 A:THR633 4.4 33.3 1.0
O A:HOH931 4.4 28.9 1.0
OD2 A:ASP674 4.5 32.6 1.0
CB A:ASP564 4.5 32.4 1.0
O A:HOH960 4.5 37.3 1.0
O A:THR633 4.5 40.5 1.0
NE2 A:HIS567 4.5 33.0 1.0
NE2 A:HIS563 4.6 31.6 1.0
CD A:GLU592 4.6 32.9 1.0
CB A:THR633 4.6 34.1 1.0
CG A:GLU592 4.6 33.3 1.0
CA A:ASP564 4.8 33.1 1.0
NE2 A:HIS525 4.8 38.4 1.0
CD2 A:HIS525 4.9 40.1 1.0

Magnesium binding site 2 out of 4 in 5sjl

Go back to Magnesium Binding Sites List in 5sjl
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.0
occ:1.00
 O B:HOH967 1.7 34.0 1.0
O B:HOH934 1.9 23.3 1.0
O B:HOH980 2.0 24.9 1.0
O B:HOH920 2.1 27.3 1.0
O B:HOH936 2.2 24.4 1.0
OD1 B:ASP564 2.2 25.7 1.0
CG B:ASP564 3.2 27.0 1.0
OD2 B:ASP564 3.5 29.3 1.0
ZN B:ZN801 3.8 32.8 1.0
OE2 B:GLU592 4.0 27.8 1.0
NE2 B:HIS595 4.1 31.3 1.0
CD2 B:HIS567 4.3 35.5 1.0
O B:HOH921 4.3 29.8 1.0
O B:THR633 4.3 31.0 1.0
OG1 B:THR633 4.3 29.2 1.0
CD2 B:HIS563 4.3 27.4 1.0
NE2 B:HIS567 4.3 37.1 1.0
O B:HIS563 4.4 29.4 1.0
CD2 B:HIS595 4.4 31.4 1.0
OD2 B:ASP674 4.4 35.6 1.0
CB B:ASP564 4.5 27.1 1.0
CD2 B:HIS525 4.7 32.3 1.0
NE2 B:HIS563 4.7 26.3 1.0
CB B:THR633 4.8 28.8 1.0
CG B:GLU592 4.8 31.7 1.0
CA B:ASP564 4.8 28.5 1.0
NE2 B:HIS525 4.8 29.4 1.0
CD B:GLU592 4.8 31.1 1.0

Magnesium binding site 3 out of 4 in 5sjl

Go back to Magnesium Binding Sites List in 5sjl
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:31.8
occ:1.00
 O C:HOH948 2.0 37.4 1.0
O C:HOH957 2.0 34.8 1.0
OD1 C:ASP564 2.0 33.7 1.0
O C:HOH908 2.0 35.0 1.0
O C:HOH923 2.1 23.8 1.0
O C:HOH906 2.4 28.5 1.0
CG C:ASP564 3.0 32.3 1.0
OD2 C:ASP564 3.3 33.8 1.0
OE2 C:GLU592 3.8 36.3 1.0
ZN C:ZN801 3.9 38.2 1.0
NE2 C:HIS595 4.0 35.8 1.0
CD2 C:HIS567 4.0 36.6 1.0
O C:HOH954 4.2 28.3 1.0
NE2 C:HIS567 4.2 35.0 1.0
CB C:ASP564 4.4 26.9 1.0
CD2 C:HIS595 4.4 36.2 1.0
CD2 C:HIS525 4.4 32.6 1.0
OG1 C:THR633 4.4 25.7 1.0
CD2 C:HIS563 4.4 31.6 1.0
OD2 C:ASP674 4.5 30.6 1.0
NE2 C:HIS525 4.5 31.7 1.0
O C:HIS563 4.5 29.0 1.0
O C:THR633 4.7 31.8 1.0
NE2 C:HIS563 4.8 31.0 1.0
CD C:GLU592 4.8 39.0 1.0
CA C:ASP564 4.8 29.7 1.0
CB C:THR633 4.9 30.2 1.0
CG C:GLU592 5.0 36.5 1.0

Magnesium binding site 4 out of 4 in 5sjl

Go back to Magnesium Binding Sites List in 5sjl
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-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 6- Cyclopropyl-N-[4-[(2-Hydroxy-2-Methylpropyl)Carbamoyl]Pyridin-3-Yl]- 3-(Pyrimidin-5-Ylamino)Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:36.3
occ:1.00
 O D:HOH926 2.0 33.9 1.0
O D:HOH902 2.0 35.0 1.0
O D:HOH932 2.1 28.8 1.0
O D:HOH927 2.1 36.6 1.0
OD1 D:ASP564 2.2 37.7 1.0
O D:HOH903 2.3 26.5 1.0
CG D:ASP564 3.1 33.9 1.0
OD2 D:ASP564 3.3 37.6 1.0
O D:HOH946 3.5 37.1 1.0
ZN D:ZN801 3.7 39.8 1.0
CD2 D:HIS563 4.2 39.1 1.0
OE2 D:GLU592 4.2 38.1 1.0
OD2 D:ASP674 4.2 39.8 1.0
NE2 D:HIS595 4.3 38.8 1.0
CB D:ASP564 4.4 33.0 1.0
CD2 D:HIS567 4.4 38.0 1.0
OG1 D:THR633 4.5 35.0 1.0
CD2 D:HIS525 4.5 40.7 1.0
O D:THR633 4.5 36.9 1.0
NE2 D:HIS567 4.6 38.4 1.0
CD2 D:HIS595 4.6 37.7 1.0
NE2 D:HIS525 4.6 42.5 1.0
O D:HIS563 4.6 31.4 1.0
NE2 D:HIS563 4.6 37.5 1.0
CB D:THR633 4.7 36.9 1.0
CA D:ASP564 4.9 33.0 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 04:24:15 2024

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