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Magnesium in PDB 5skn: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide, PDB code: 5skn 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) 35.03 / 1.90
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.48, 135.48, 235.361, 90, 90, 120
R / Rfree (%) 19.1 / 22.2

Other elements in 5skn:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Zinc (Zn) 4 atoms
Fluorine (F) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide (pdb code 5skn). 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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide, PDB code: 5skn:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skn

Go back to Magnesium Binding Sites List in 5skn
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:20.0
occ:1.00
 O A:HOH946 2.0 19.4 1.0
O A:HOH1028 2.0 22.2 1.0
O A:HOH936 2.0 21.9 1.0
OD1 A:ASP564 2.0 20.6 1.0
O A:HOH977 2.2 18.1 1.0
O A:HOH963 2.2 25.2 1.0
CG A:ASP564 3.1 21.1 1.0
OD2 A:ASP564 3.5 21.3 1.0
ZN A:ZN801 3.8 25.4 1.0
O A:HOH1027 3.8 41.5 1.0
OE2 A:GLU592 4.0 24.2 1.0
NE2 A:HIS595 4.0 22.9 1.0
O A:HOH1010 4.1 26.0 1.0
CD2 A:HIS567 4.2 22.6 1.0
OG1 A:THR633 4.2 24.3 1.0
O A:HOH1020 4.3 29.6 1.0
CD2 A:HIS595 4.3 21.7 1.0
CD2 A:HIS563 4.3 20.8 1.0
O A:HIS563 4.4 21.8 1.0
NE2 A:HIS567 4.4 22.3 1.0
CB A:ASP564 4.4 20.8 1.0
OD2 A:ASP674 4.4 26.9 1.0
O A:THR633 4.5 24.3 1.0
NE2 A:HIS525 4.6 23.3 1.0
CD2 A:HIS525 4.6 23.8 1.0
CB A:THR633 4.7 24.4 1.0
NE2 A:HIS563 4.8 21.1 1.0
CA A:ASP564 4.8 21.3 1.0
CG A:GLU592 4.9 23.4 1.0
CD A:GLU592 4.9 23.7 1.0

Magnesium binding site 2 out of 4 in 5skn

Go back to Magnesium Binding Sites List in 5skn
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:17.0
occ:1.00
 O B:HOH959 1.9 19.9 1.0
O B:HOH915 2.0 18.7 1.0
O B:HOH920 2.0 17.9 1.0
O B:HOH1027 2.1 19.7 1.0
OD1 B:ASP564 2.1 19.1 1.0
O B:HOH1005 2.1 14.9 1.0
CG B:ASP564 3.1 18.6 1.0
OD2 B:ASP564 3.4 17.7 1.0
ZN B:ZN801 3.8 24.6 1.0
OE2 B:GLU592 3.9 27.0 1.0
O B:HOH1039 4.0 33.4 1.0
NE2 B:HIS595 4.1 22.5 1.0
O B:HOH1004 4.1 26.0 1.0
OG1 B:THR633 4.2 21.8 1.0
CD2 B:HIS563 4.2 20.5 1.0
CD2 B:HIS567 4.3 21.4 1.0
O B:HIS563 4.3 21.9 1.0
OD2 B:ASP674 4.3 23.1 1.0
O B:HOH996 4.3 27.5 1.0
CD2 B:HIS595 4.3 22.6 1.0
NE2 B:HIS567 4.4 21.0 1.0
O B:THR633 4.4 21.2 1.0
CB B:ASP564 4.4 18.6 1.0
NE2 B:HIS563 4.5 20.0 1.0
CD2 B:HIS525 4.6 23.9 1.0
NE2 B:HIS525 4.7 24.8 1.0
CB B:THR633 4.7 20.6 1.0
CA B:ASP564 4.8 19.0 1.0
CD B:GLU592 4.8 23.8 1.0
CG B:GLU592 4.8 23.9 1.0

Magnesium binding site 3 out of 4 in 5skn

Go back to Magnesium Binding Sites List in 5skn
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:24.5
occ:1.00
 O C:HOH977 2.0 23.9 1.0
O C:HOH1005 2.1 23.4 1.0
OD1 C:ASP564 2.1 23.1 1.0
O C:HOH917 2.1 21.8 1.0
O C:HOH1047 2.1 23.1 1.0
O C:HOH951 2.2 20.7 1.0
CG C:ASP564 3.1 22.2 1.0
OD2 C:ASP564 3.5 22.8 1.0
ZN C:ZN801 3.8 27.1 1.0
OE2 C:GLU592 4.1 26.3 1.0
NE2 C:HIS595 4.1 25.0 1.0
O C:HOH1040 4.1 28.1 1.0
O C:HOH1062 4.1 38.6 1.0
CD2 C:HIS567 4.2 25.3 1.0
CD2 C:HIS563 4.2 21.0 1.0
OG1 C:THR633 4.2 24.2 1.0
O C:HIS563 4.3 22.2 1.0
CD2 C:HIS595 4.3 23.2 1.0
O C:HOH1028 4.3 31.9 1.0
OD2 C:ASP674 4.4 27.3 1.0
NE2 C:HIS567 4.4 26.6 1.0
CB C:ASP564 4.5 21.5 1.0
O C:THR633 4.5 24.8 1.0
NE2 C:HIS563 4.6 21.8 1.0
CB C:THR633 4.7 24.6 1.0
CD2 C:HIS525 4.7 28.7 1.0
NE2 C:HIS525 4.7 29.8 1.0
CA C:ASP564 4.8 22.2 1.0
CG C:GLU592 4.8 25.3 1.0
CD C:GLU592 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 5skn

Go back to Magnesium Binding Sites List in 5skn
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide


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 N-[3- [3-[2-(2-Fluorophenyl)Pyrazol-3-Yl]-4-Oxopyridazin-1- Yl]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.2
occ:1.00
 O D:HOH981 1.9 21.9 1.0
O D:HOH977 2.1 31.3 1.0
OD1 D:ASP564 2.1 27.9 1.0
O D:HOH929 2.1 25.3 1.0
O D:HOH945 2.1 25.3 1.0
O D:HOH927 2.2 30.8 1.0
CG D:ASP564 3.1 27.4 1.0
OD2 D:ASP564 3.4 28.6 1.0
ZN D:ZN801 3.8 33.7 1.0
O D:HOH1000 4.0 36.5 1.0
OE2 D:GLU592 4.0 35.1 1.0
O D:HOH991 4.1 28.9 1.0
NE2 D:HIS595 4.1 31.1 1.0
CD2 D:HIS567 4.2 35.3 1.0
OG1 D:THR633 4.3 29.4 1.0
NE2 D:HIS567 4.3 32.5 1.0
CD2 D:HIS595 4.4 31.5 1.0
CD2 D:HIS563 4.4 30.1 1.0
O D:HIS563 4.4 31.8 1.0
OD2 D:ASP674 4.4 33.0 1.0
CB D:ASP564 4.5 27.4 1.0
O D:THR633 4.5 30.9 1.0
CD2 D:HIS525 4.5 35.4 1.0
NE2 D:HIS525 4.6 37.0 1.0
NE2 D:HIS563 4.7 28.9 1.0
CB D:THR633 4.8 30.5 1.0
CA D:ASP564 4.8 27.2 1.0
CG D:GLU592 4.8 33.6 1.0
CD D:GLU592 4.9 34.0 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 04:37:38 2024

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