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

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy