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Magnesium in PDB 5ski: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5ski was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.236, 135.236, 235.217, 90, 90, 120
R / Rfree (%) 17.8 / 22.8

Other elements in 5ski:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine 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 N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine (pdb code 5ski). 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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5ski:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ski

Go back to Magnesium Binding Sites List in 5ski
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.5
occ:1.00
 O A:HOH983 1.9 31.1 1.0
O A:HOH978 2.0 29.6 1.0
O A:HOH917 2.1 24.1 1.0
OD1 A:ASP564 2.1 29.8 1.0
O A:HOH911 2.1 28.4 1.0
O A:HOH928 2.2 26.6 1.0
CG A:ASP564 3.1 28.5 1.0
OD2 A:ASP564 3.4 32.2 1.0
ZN A:ZN801 3.8 35.4 1.0
O A:HOH942 3.8 45.8 1.0
OE2 A:GLU592 3.9 31.4 1.0
NE2 A:HIS595 4.0 29.4 1.0
O A:HOH988 4.2 31.2 1.0
CD2 A:HIS563 4.2 28.0 1.0
OG1 A:THR633 4.3 33.8 1.0
CD2 A:HIS567 4.4 29.1 1.0
CD2 A:HIS595 4.4 29.4 1.0
O A:HIS563 4.4 29.0 1.0
CB A:ASP564 4.4 28.6 1.0
CD2 A:HIS525 4.5 34.7 1.0
O A:THR633 4.5 36.8 1.0
NE2 A:HIS525 4.5 34.0 1.0
OD2 A:ASP674 4.6 36.9 1.0
NE2 A:HIS563 4.6 26.7 1.0
NE2 A:HIS567 4.6 28.7 1.0
CB A:THR633 4.8 30.7 1.0
CA A:ASP564 4.8 30.8 1.0
CD A:GLU592 4.8 32.0 1.0
CG A:GLU592 4.8 29.3 1.0

Magnesium binding site 2 out of 4 in 5ski

Go back to Magnesium Binding Sites List in 5ski
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.4
occ:1.00
 O B:HOH953 1.8 21.4 1.0
O B:HOH957 1.9 29.4 1.0
O B:HOH902 2.0 24.1 1.0
O B:HOH1009 2.1 25.5 1.0
O B:HOH960 2.1 28.1 1.0
OD1 B:ASP564 2.1 25.7 1.0
CG B:ASP564 3.2 25.8 1.0
OD2 B:ASP564 3.6 25.7 1.0
ZN B:ZN801 3.8 33.2 1.0
OE2 B:GLU592 3.8 27.0 1.0
NE2 B:HIS595 4.0 30.5 1.0
CD2 B:HIS567 4.2 29.6 1.0
OG1 B:THR633 4.3 32.0 1.0
CD2 B:HIS563 4.3 29.8 1.0
CD2 B:HIS595 4.3 32.5 1.0
O B:HOH990 4.3 25.8 1.0
NE2 B:HIS567 4.4 30.4 1.0
O B:HIS563 4.4 29.0 1.0
OD2 B:ASP674 4.4 36.4 1.0
CB B:ASP564 4.5 26.4 1.0
O B:THR633 4.6 25.8 1.0
CB B:THR633 4.6 28.8 1.0
NE2 B:HIS563 4.6 28.2 1.0
CD2 B:HIS525 4.7 31.1 1.0
NE2 B:HIS525 4.7 32.9 1.0
CG B:GLU592 4.7 28.5 1.0
CD B:GLU592 4.7 30.7 1.0
CA B:ASP564 4.7 27.6 1.0

Magnesium binding site 3 out of 4 in 5ski

Go back to Magnesium Binding Sites List in 5ski
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.6
occ:1.00
 O C:HOH966 1.9 31.1 1.0
O C:HOH952 2.0 26.6 1.0
O C:HOH938 2.1 27.4 1.0
OD1 C:ASP564 2.1 26.3 1.0
O C:HOH930 2.1 26.4 1.0
O C:HOH981 2.2 29.5 1.0
CG C:ASP564 3.2 27.9 1.0
OD2 C:ASP564 3.6 29.3 1.0
O C:HOH1014 3.8 59.0 1.0
ZN C:ZN801 3.9 34.6 1.0
OE2 C:GLU592 3.9 28.3 1.0
NE2 C:HIS595 4.0 31.2 1.0
O C:HOH969 4.0 41.4 1.0
CD2 C:HIS567 4.1 31.6 1.0
OG1 C:THR633 4.2 30.8 1.0
O C:HIS563 4.2 27.5 1.0
NE2 C:HIS567 4.3 33.5 1.0
CD2 C:HIS595 4.3 27.5 1.0
CD2 C:HIS563 4.3 25.5 1.0
O C:HOH973 4.4 30.9 1.0
OD2 C:ASP674 4.4 39.8 1.0
CB C:ASP564 4.5 26.6 1.0
O C:THR633 4.5 31.3 1.0
CD2 C:HIS525 4.6 34.0 1.0
NE2 C:HIS525 4.6 35.0 1.0
CB C:THR633 4.8 32.0 1.0
CD C:GLU592 4.8 32.4 1.0
CG C:GLU592 4.8 33.1 1.0
CA C:ASP564 4.8 27.9 1.0
NE2 C:HIS563 4.8 28.7 1.0

Magnesium binding site 4 out of 4 in 5ski

Go back to Magnesium Binding Sites List in 5ski
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:38.1
occ:1.00
 O D:HOH944 2.1 31.3 1.0
O D:HOH968 2.1 31.8 1.0
O D:HOH906 2.1 36.0 1.0
OD1 D:ASP564 2.2 38.2 1.0
O D:HOH926 2.2 32.6 1.0
O D:HOH915 2.2 32.6 1.0
CG D:ASP564 3.2 34.2 1.0
OD2 D:ASP564 3.5 41.2 1.0
ZN D:ZN801 3.7 40.4 1.0
O D:HOH931 3.8 43.0 1.0
OE2 D:GLU592 3.9 40.9 1.0
NE2 D:HIS595 4.0 40.8 1.0
O D:HOH959 4.1 43.1 1.0
OG1 D:THR633 4.1 38.7 1.0
CD2 D:HIS567 4.2 41.7 1.0
CD2 D:HIS595 4.3 40.6 1.0
CD2 D:HIS563 4.3 31.3 1.0
O D:HIS563 4.4 38.4 1.0
CD2 D:HIS525 4.4 45.1 1.0
OD2 D:ASP674 4.5 42.3 1.0
NE2 D:HIS567 4.5 41.2 1.0
CB D:ASP564 4.5 31.9 1.0
O D:THR633 4.5 45.2 1.0
NE2 D:HIS525 4.5 42.3 1.0
CB D:THR633 4.7 40.2 1.0
NE2 D:HIS563 4.8 32.9 1.0
CD D:GLU592 4.8 41.9 1.0
CA D:ASP564 4.8 34.6 1.0
CG D:GLU592 4.9 44.6 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 04:35:11 2024

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