Atomistry » Magnesium » PDB 5sh3-5si6 » 5sh8
Atomistry »
  Magnesium »
    PDB 5sh3-5si6 »
      5sh8 »

Magnesium in PDB 5sh8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8 was solved by C.Joseph, J.Benz, A.Flohr, E.Vieira, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.54 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.51, 135.51, 235.29, 90, 90, 120
R / Rfree (%) 16 / 18.6

Other elements in 5sh8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide also contains other interesting chemical elements:

Praseodymium (Pr) 3 atoms
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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide (pdb code 5sh8). 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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide, PDB code: 5sh8:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:24.0
occ:1.00
 O A:HOH944 1.9 22.4 1.0
OD1 A:ASP564 1.9 24.8 1.0
O A:HOH1013 2.0 27.1 1.0
O A:HOH986 2.0 29.0 1.0
O A:HOH973 2.1 15.3 1.0
O A:HOH959 2.2 27.0 1.0
CG A:ASP564 3.0 24.6 1.0
OD2 A:ASP564 3.4 26.7 1.0
OE2 A:GLU592 3.8 33.3 1.0
ZN A:ZN802 3.9 30.2 1.0
NE2 A:HIS595 4.0 25.8 1.0
O A:HOH958 4.2 35.6 1.0
CD2 A:HIS563 4.2 23.7 1.0
CD2 A:HIS595 4.2 21.3 1.0
OG1 A:THR633 4.2 29.0 1.0
O A:HIS563 4.2 24.0 1.0
O A:HOH1001 4.3 30.9 1.0
CB A:ASP564 4.3 24.3 1.0
CD2 A:HIS567 4.3 32.0 1.0
NE2 A:HIS563 4.5 22.5 1.0
NE2 A:HIS567 4.6 27.7 1.0
CA A:ASP564 4.6 25.7 1.0
CD A:GLU592 4.7 30.7 1.0
CG A:GLU592 4.7 29.2 1.0
CB A:THR633 4.7 25.4 1.0
OD2 A:ASP674 4.7 31.4 1.0
O A:THR633 4.7 28.1 1.0
CD2 A:HIS525 4.8 27.8 1.0
C A:HIS563 4.9 23.8 1.0

Magnesium binding site 2 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:24.6
occ:1.00
 O B:HOH952 1.9 26.2 1.0
O B:HOH965 2.0 19.4 1.0
O B:HOH1013 2.0 22.3 1.0
O B:HOH1016 2.0 21.1 1.0
OD1 B:ASP564 2.1 23.4 1.0
O B:HOH948 2.2 26.4 1.0
CG B:ASP564 3.2 22.7 1.0
O B:HOH1006 3.6 44.7 1.0
OD2 B:ASP564 3.7 23.7 1.0
ZN B:ZN802 3.8 28.2 1.0
O B:HOH1025 3.9 38.7 1.0
NE2 B:HIS595 4.1 24.5 1.0
O B:HIS563 4.1 25.1 1.0
OE2 B:GLU592 4.1 27.9 1.0
CD2 B:HIS563 4.2 16.4 1.0
CD2 B:HIS595 4.2 24.8 1.0
OG1 B:THR633 4.2 24.0 1.0
CD2 B:HIS567 4.3 25.9 1.0
OD2 B:ASP674 4.4 25.6 1.0
CB B:ASP564 4.5 24.4 1.0
O B:HOH947 4.5 36.2 1.0
O B:THR633 4.5 27.6 1.0
NE2 B:HIS567 4.5 23.9 1.0
CA B:ASP564 4.6 23.3 1.0
CB B:THR633 4.7 26.1 1.0
NE2 B:HIS563 4.7 22.6 1.0
CD2 B:HIS525 4.8 26.1 1.0
NE2 B:HIS525 4.9 29.1 1.0
CG B:GLU592 4.9 27.3 1.0
C B:HIS563 4.9 23.6 1.0
CD B:GLU592 4.9 27.9 1.0

Magnesium binding site 3 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:21.7
occ:1.00
 O C:HOH981 2.0 26.1 1.0
O C:HOH952 2.1 31.9 1.0
OD1 C:ASP564 2.1 22.3 1.0
O C:HOH975 2.1 23.4 1.0
O C:HOH1008 2.1 20.7 1.0
O C:HOH908 2.2 26.1 1.0
CG C:ASP564 3.1 23.5 1.0
OD2 C:ASP564 3.5 21.4 1.0
ZN C:ZN802 3.8 31.8 1.0
O C:HOH979 3.9 41.1 1.0
NE2 C:HIS595 4.0 26.2 1.0
O C:HOH1025 4.0 42.8 1.0
OE2 C:GLU592 4.1 29.4 1.0
O C:HIS563 4.1 26.3 1.0
NE2 C:HIS567 4.2 31.6 1.0
OG1 C:THR633 4.2 28.2 1.0
CD2 C:HIS567 4.2 33.5 1.0
CD2 C:HIS563 4.3 26.7 1.0
CD2 C:HIS595 4.3 24.3 1.0
CB C:ASP564 4.4 27.6 1.0
OD2 C:ASP674 4.5 29.4 1.0
O C:HOH977 4.5 47.9 1.0
O C:THR633 4.6 31.8 1.0
NE2 C:HIS563 4.7 25.3 1.0
CD2 C:HIS525 4.7 27.2 1.0
CB C:THR633 4.7 27.2 1.0
CA C:ASP564 4.7 25.0 1.0
NE2 C:HIS525 4.8 32.2 1.0
CG C:GLU592 4.8 27.6 1.0
CD C:GLU592 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 5sh8

Go back to Magnesium Binding Sites List in 5sh8
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6- Methyl-N-(5-Methyl-2-Phenylpyrazol-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- Methyl-N-(5-Methyl-2-Phenylpyrazol-3-Yl)-3-(Pyrimidin-5-Ylamino) Pyridine-2-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:26.6
occ:1.00
 O D:HOH1003 2.0 22.6 1.0
OD1 D:ASP564 2.1 25.4 1.0
O D:HOH918 2.1 34.4 1.0
O D:HOH935 2.1 22.9 1.0
O D:HOH943 2.1 24.4 1.0
O D:HOH971 2.2 20.9 1.0
CG D:ASP564 3.1 29.2 1.0
OD2 D:ASP564 3.5 34.0 1.0
ZN D:ZN802 3.8 33.2 1.0
O D:HOH946 3.9 31.4 1.0
OE2 D:GLU592 4.1 33.1 1.0
NE2 D:HIS595 4.2 29.5 1.0
CD2 D:HIS567 4.2 33.2 1.0
O D:HOH982 4.2 33.6 1.0
OG1 D:THR633 4.2 37.0 1.0
NE2 D:HIS567 4.3 27.1 1.0
CB D:ASP564 4.4 28.9 1.0
CD2 D:HIS595 4.5 30.9 1.0
O D:HIS563 4.6 31.1 1.0
CD2 D:HIS525 4.6 42.5 1.0
CD2 D:HIS563 4.6 32.3 1.0
OD2 D:ASP674 4.6 30.3 1.0
O D:THR633 4.7 41.0 1.0
CA D:ASP564 4.7 28.7 1.0
NE2 D:HIS525 4.8 36.2 1.0
CB D:THR633 4.8 38.2 1.0
NE2 D:HIS563 4.9 27.4 1.0
CG D:GLU592 4.9 34.5 1.0
CD D:GLU592 5.0 37.0 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: Tue Aug 12 19:46:15 2025

Last articles

Zn in 9UUO
Zn in 9UUS
Zn in 9W4R
Zn in 9VKW
Zn in 9W4S
Zn in 9VH1
Zn in 9RMX
Zn in 9RMU
Zn in 9QWN
Zn in 9U9Y
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy