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Magnesium in PDB 5sgw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One, PDB code: 5sgw was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.56 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.589, 135.589, 235.349, 90, 90, 120
R / Rfree (%) 18.7 / 21.6

Other elements in 5sgw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One 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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One (pdb code 5sgw). 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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One, PDB code: 5sgw:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sgw

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:21.3
occ:1.00
 O A:HOH1039 1.9 22.5 1.0
O A:HOH926 2.0 20.3 1.0
OD1 A:ASP564 2.0 20.3 1.0
O A:HOH945 2.0 19.6 1.0
O A:HOH976 2.1 19.2 1.0
O A:HOH939 2.2 20.3 1.0
CG A:ASP564 3.0 21.4 1.0
OD2 A:ASP564 3.4 21.2 1.0
ZN A:ZN801 3.7 25.6 1.0
O A:HOH1024 3.9 47.2 1.0
NE2 A:HIS595 4.0 21.4 1.0
O A:HOH1008 4.1 25.9 1.0
OE2 A:GLU592 4.1 25.1 1.0
CD2 A:HIS563 4.2 19.6 1.0
OG1 A:THR633 4.3 22.0 1.0
CD2 A:HIS567 4.3 23.1 1.0
O A:HOH994 4.3 31.7 1.0
O A:HIS563 4.3 20.9 1.0
CD2 A:HIS595 4.3 20.9 1.0
CB A:ASP564 4.4 21.2 1.0
OD2 A:ASP674 4.4 28.4 1.0
NE2 A:HIS567 4.4 22.6 1.0
CD2 A:HIS525 4.6 22.7 1.0
NE2 A:HIS525 4.6 23.9 1.0
NE2 A:HIS563 4.6 21.1 1.0
O A:THR633 4.6 23.6 1.0
CA A:ASP564 4.7 21.2 1.0
CB A:THR633 4.7 22.2 1.0
CG A:GLU592 4.8 23.4 1.0
CD A:GLU592 4.9 24.8 1.0

Magnesium binding site 2 out of 4 in 5sgw

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:17.3
occ:1.00
 O B:HOH956 2.0 18.1 1.0
O B:HOH914 2.0 16.3 1.0
O B:HOH950 2.1 18.4 1.0
O B:HOH1022 2.1 17.3 1.0
OD1 B:ASP564 2.1 20.0 1.0
O B:HOH1024 2.1 18.5 1.0
CG B:ASP564 3.1 19.4 1.0
OD2 B:ASP564 3.4 18.6 1.0
ZN B:ZN801 3.7 23.7 1.0
O B:HOH1048 4.0 41.1 1.0
OE2 B:GLU592 4.0 26.4 1.0
NE2 B:HIS595 4.1 20.6 1.0
O B:HOH1017 4.1 25.5 1.0
CD2 B:HIS563 4.2 18.5 1.0
OG1 B:THR633 4.2 20.1 1.0
CD2 B:HIS567 4.3 23.9 1.0
O B:HIS563 4.3 19.9 1.0
O B:HOH985 4.3 25.9 1.0
OD2 B:ASP674 4.3 23.6 1.0
CD2 B:HIS595 4.3 22.2 1.0
NE2 B:HIS567 4.4 22.1 1.0
CB B:ASP564 4.4 18.8 1.0
O B:THR633 4.5 20.8 1.0
NE2 B:HIS563 4.5 18.4 1.0
CD2 B:HIS525 4.6 22.6 1.0
NE2 B:HIS525 4.6 23.0 1.0
CB B:THR633 4.6 20.1 1.0
CA B:ASP564 4.8 19.1 1.0
CG B:GLU592 4.8 23.4 1.0
CD B:GLU592 4.9 24.1 1.0

Magnesium binding site 3 out of 4 in 5sgw

Go back to Magnesium Binding Sites List in 5sgw
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:23.4
occ:1.00
 OD1 C:ASP564 2.0 20.6 1.0
O C:HOH954 2.1 20.7 1.0
O C:HOH914 2.1 18.7 1.0
O C:HOH1001 2.1 21.1 1.0
O C:HOH1041 2.1 19.7 1.0
O C:HOH942 2.2 20.0 1.0
CG C:ASP564 3.1 20.9 1.0
OD2 C:ASP564 3.5 20.8 1.0
ZN C:ZN801 3.8 24.8 1.0
NE2 C:HIS595 4.1 22.7 1.0
OE2 C:GLU592 4.1 25.7 1.0
O C:HOH1048 4.1 45.4 1.0
CD2 C:HIS563 4.1 21.1 1.0
O C:HOH1018 4.2 26.1 1.0
OG1 C:THR633 4.2 22.0 1.0
CD2 C:HIS567 4.2 24.2 1.0
O C:HIS563 4.3 21.6 1.0
OD2 C:ASP674 4.3 28.2 1.0
CD2 C:HIS595 4.3 22.3 1.0
O C:HOH999 4.4 27.5 1.0
CB C:ASP564 4.4 20.6 1.0
NE2 C:HIS567 4.5 24.6 1.0
O C:THR633 4.5 22.1 1.0
NE2 C:HIS563 4.5 21.1 1.0
CB C:THR633 4.7 22.1 1.0
CD2 C:HIS525 4.7 24.8 1.0
NE2 C:HIS525 4.7 24.8 1.0
CA C:ASP564 4.8 21.0 1.0
CG C:GLU592 4.8 24.5 1.0
CD C:GLU592 4.8 25.5 1.0

Magnesium binding site 4 out of 4 in 5sgw

Go back to Magnesium Binding Sites List in 5sgw
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One


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 2- Phenyl-6-(2-Phenylpyrazol-3-Yl)-3,4-Dihydropyridazin-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:27.8
occ:1.00
 O D:HOH993 2.0 20.5 1.0
OD1 D:ASP564 2.1 25.6 1.0
O D:HOH933 2.1 23.8 1.0
O D:HOH984 2.1 25.6 1.0
O D:HOH908 2.1 21.6 1.0
O D:HOH930 2.2 24.6 1.0
CG D:ASP564 3.1 25.0 1.0
OD2 D:ASP564 3.5 23.9 1.0
ZN D:ZN801 3.8 28.9 1.0
O D:HOH990 4.0 26.7 1.0
NE2 D:HIS595 4.0 26.4 1.0
OE2 D:GLU592 4.1 30.6 1.0
O D:HOH975 4.2 35.9 1.0
CD2 D:HIS567 4.2 29.8 1.0
OG1 D:THR633 4.2 27.1 1.0
CD2 D:HIS595 4.2 26.4 1.0
CD2 D:HIS563 4.3 23.9 1.0
O D:HIS563 4.3 24.8 1.0
OD2 D:ASP674 4.4 28.9 1.0
NE2 D:HIS567 4.4 27.9 1.0
CB D:ASP564 4.5 24.1 1.0
O D:THR633 4.5 28.3 1.0
CD2 D:HIS525 4.5 30.7 1.0
NE2 D:HIS525 4.6 32.8 1.0
NE2 D:HIS563 4.6 22.8 1.0
CB D:THR633 4.7 28.1 1.0
CA D:ASP564 4.8 25.3 1.0
CG D:GLU592 4.9 29.2 1.0
CD D:GLU592 4.9 29.3 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 19:42:44 2025

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