Magnesium in PDB 5ske: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide, PDB code: 5ske 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) 43.46 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.086, 135.086, 235.075, 90, 90, 120
R / Rfree (%) 17.7 / 21.5

Other elements in 5ske:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide also contains other interesting chemical elements:

Fluorine (F) 12 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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide (pdb code 5ske). 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- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide, PDB code: 5ske:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5ske

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.6
occ:1.00
 O A:HOH923 1.9 21.8 1.0
OD1 A:ASP564 2.0 27.4 1.0
O A:HOH955 2.0 30.2 1.0
O A:HOH951 2.0 26.7 1.0
O A:HOH937 2.0 33.4 1.0
O A:HOH996 2.1 26.6 1.0
CG A:ASP564 3.0 29.1 1.0
OD2 A:ASP564 3.3 31.3 1.0
ZN A:ZN801 3.9 33.5 1.0
OE2 A:GLU592 4.0 35.0 1.0
NE2 A:HIS595 4.0 28.7 1.0
CD2 A:HIS595 4.2 29.6 1.0
O A:HOH974 4.2 30.4 1.0
OG1 A:THR633 4.2 31.3 1.0
O A:HIS563 4.2 32.3 1.0
CD2 A:HIS563 4.2 26.8 1.0
CD2 A:HIS567 4.2 38.0 1.0
O A:HOH934 4.3 42.0 1.0
CB A:ASP564 4.4 27.8 1.0
O A:THR633 4.5 33.0 1.0
NE2 A:HIS567 4.5 37.7 1.0
OD2 A:ASP674 4.5 38.6 1.0
NE2 A:HIS563 4.6 27.9 1.0
CB A:THR633 4.7 31.7 1.0
CG A:GLU592 4.7 33.6 1.0
CA A:ASP564 4.7 29.9 1.0
CD A:GLU592 4.8 35.2 1.0
CD2 A:HIS525 4.8 31.2 1.0
NE2 A:HIS525 4.8 30.8 1.0
C A:HIS563 5.0 29.4 1.0

Magnesium binding site 2 out of 4 in 5ske

Go back to Magnesium Binding Sites List in 5ske
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.4
occ:1.00
 O B:HOH941 1.9 26.6 1.0
O B:HOH974 2.1 28.3 1.0
OD1 B:ASP564 2.1 29.9 1.0
O B:HOH946 2.2 26.5 1.0
O B:HOH919 2.2 29.3 1.0
O B:HOH916 2.2 23.8 1.0
CG B:ASP564 3.1 28.8 1.0
OD2 B:ASP564 3.5 27.2 1.0
O B:HOH999 3.9 30.9 1.0
ZN B:ZN801 3.9 32.7 1.0
NE2 B:HIS595 4.0 32.2 1.0
OE2 B:GLU592 4.1 31.4 1.0
CD2 B:HIS567 4.2 29.8 1.0
CD2 B:HIS595 4.2 33.6 1.0
OG1 B:THR633 4.3 30.2 1.0
NE2 B:HIS567 4.3 29.4 1.0
CD2 B:HIS563 4.3 27.4 1.0
O B:HIS563 4.3 32.1 1.0
O B:HOH977 4.4 42.4 1.0
OD2 B:ASP674 4.4 29.8 1.0
CB B:ASP564 4.5 28.2 1.0
O B:THR633 4.6 29.2 1.0
NE2 B:HIS525 4.6 28.6 1.0
CD2 B:HIS525 4.6 29.2 1.0
CB B:THR633 4.7 30.0 1.0
NE2 B:HIS563 4.7 28.7 1.0
CA B:ASP564 4.8 29.6 1.0
CG B:GLU592 4.8 29.7 1.0
CD B:GLU592 4.8 30.5 1.0

Magnesium binding site 3 out of 4 in 5ske

Go back to Magnesium Binding Sites List in 5ske
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:28.0
occ:1.00
 OD1 C:ASP564 2.0 30.5 1.0
O C:HOH928 2.1 33.1 1.0
O C:HOH962 2.1 29.1 1.0
O C:HOH938 2.1 27.0 1.0
O C:HOH930 2.1 25.8 1.0
O C:HOH976 2.2 34.0 1.0
CG C:ASP564 2.9 30.1 1.0
OD2 C:ASP564 3.2 29.2 1.0
ZN C:ZN801 3.8 35.7 1.0
O C:HOH982 3.9 32.4 1.0
NE2 C:HIS595 4.1 31.4 1.0
O C:HIS563 4.2 29.5 1.0
CD2 C:HIS567 4.2 33.3 1.0
CD2 C:HIS563 4.2 29.3 1.0
OE2 C:GLU592 4.2 33.1 1.0
OG1 C:THR633 4.3 33.8 1.0
CB C:ASP564 4.3 29.1 1.0
CD2 C:HIS595 4.3 32.7 1.0
OD2 C:ASP674 4.4 32.9 1.0
NE2 C:HIS567 4.4 33.7 1.0
O C:HOH969 4.5 37.7 1.0
O C:THR633 4.5 31.9 1.0
NE2 C:HIS563 4.6 29.8 1.0
CA C:ASP564 4.7 29.7 1.0
CD2 C:HIS525 4.7 33.8 1.0
NE2 C:HIS525 4.7 34.1 1.0
CB C:THR633 4.8 34.5 1.0
CG C:GLU592 4.9 33.1 1.0
C C:HIS563 5.0 28.3 1.0

Magnesium binding site 4 out of 4 in 5ske

Go back to Magnesium Binding Sites List in 5ske
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.4
occ:1.00
 O D:HOH919 2.0 33.0 1.0
O D:HOH948 2.1 28.4 1.0
O D:HOH954 2.1 23.6 1.0
O D:HOH958 2.1 35.9 1.0
O D:HOH911 2.1 35.9 1.0
OD1 D:ASP564 2.2 34.1 1.0
CG D:ASP564 3.1 35.6 1.0
OD2 D:ASP564 3.5 36.6 1.0
O D:HOH965 3.7 43.9 1.0
ZN D:ZN801 3.8 40.5 1.0
OE2 D:GLU592 4.1 38.0 1.0
OG1 D:THR633 4.1 36.2 1.0
NE2 D:HIS595 4.1 41.7 1.0
CD2 D:HIS567 4.3 43.0 1.0
CD2 D:HIS563 4.3 34.3 1.0
CD2 D:HIS595 4.4 41.8 1.0
OD2 D:ASP674 4.4 45.8 1.0
O D:THR633 4.4 42.3 1.0
NE2 D:HIS567 4.4 43.8 1.0
O D:HIS563 4.5 38.8 1.0
CB D:ASP564 4.5 36.4 1.0
CD2 D:HIS525 4.6 38.1 1.0
CB D:THR633 4.7 36.9 1.0
NE2 D:HIS525 4.7 38.1 1.0
NE2 D:HIS563 4.7 32.2 1.0
CA D:ASP564 4.8 37.2 1.0
CG D:GLU592 4.8 39.1 1.0
CD D:GLU592 4.9 39.2 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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