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Magnesium in PDB 5shs: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine, PDB code: 5shs was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.77 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.35, 135.35, 235.8, 90, 90, 120
R / Rfree (%) 16.3 / 23.3

Other elements in 5shs:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine 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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine (pdb code 5shs). 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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine, PDB code: 5shs:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shs

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.7
occ:1.00
 O A:HOH1001 1.9 30.6 1.0
OD1 A:ASP564 2.1 24.0 1.0
O A:HOH906 2.1 23.0 1.0
O A:HOH926 2.2 29.1 1.0
O A:HOH958 2.2 27.8 1.0
O A:HOH931 2.3 18.5 1.0
CG A:ASP564 3.0 27.6 1.0
OD2 A:ASP564 3.3 34.3 1.0
O A:HOH986 3.7 31.2 1.0
ZN A:ZN801 3.9 35.1 1.0
O A:HOH964 4.0 35.4 1.0
OE2 A:GLU592 4.1 32.3 1.0
NE2 A:HIS595 4.1 28.7 1.0
CD2 A:HIS567 4.4 35.1 1.0
CB A:ASP564 4.4 23.4 1.0
CD2 A:HIS563 4.5 28.9 1.0
O A:THR633 4.5 30.2 1.0
O A:HIS563 4.5 29.0 1.0
OG1 A:THR633 4.6 29.4 1.0
NE2 A:HIS525 4.6 28.3 1.0
CD2 A:HIS595 4.6 29.1 1.0
NE2 A:HIS567 4.6 34.9 1.0
CD2 A:HIS525 4.6 31.1 1.0
OD2 A:ASP674 4.7 38.2 1.0
CB A:THR633 4.8 29.2 1.0
NE2 A:HIS563 4.8 30.3 1.0
CA A:ASP564 4.9 26.3 1.0
CG A:GLU592 4.9 30.2 1.0
CD A:GLU592 4.9 32.6 1.0

Magnesium binding site 2 out of 4 in 5shs

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:19.4
occ:1.00
 O B:HOH954 1.9 18.6 1.0
O B:HOH931 1.9 17.2 1.0
O B:HOH906 2.0 15.4 1.0
O B:HOH935 2.1 20.5 1.0
OD1 B:ASP564 2.1 25.5 1.0
O B:HOH965 2.2 16.7 1.0
CG B:ASP564 3.1 29.4 1.0
OD2 B:ASP564 3.5 27.7 1.0
ZN B:ZN801 3.8 32.4 1.0
O B:HOH971 3.9 35.8 1.0
OE2 B:GLU592 3.9 27.3 1.0
NE2 B:HIS595 4.0 26.4 1.0
OG1 B:THR633 4.1 22.7 1.0
O B:HOH970 4.3 27.6 1.0
CD2 B:HIS563 4.3 26.5 1.0
O B:HIS563 4.3 32.0 1.0
OD2 B:ASP674 4.4 26.8 1.0
CD2 B:HIS567 4.4 28.6 1.0
CD2 B:HIS595 4.4 29.4 1.0
NE2 B:HIS567 4.4 29.0 1.0
CB B:ASP564 4.5 25.1 1.0
O B:THR633 4.5 27.3 1.0
CD2 B:HIS525 4.6 28.1 1.0
CB B:THR633 4.6 28.6 1.0
NE2 B:HIS563 4.6 25.3 1.0
NE2 B:HIS525 4.7 31.4 1.0
CG B:GLU592 4.7 34.4 1.0
CD B:GLU592 4.8 32.2 1.0
CA B:ASP564 4.8 28.4 1.0

Magnesium binding site 3 out of 4 in 5shs

Go back to Magnesium Binding Sites List in 5shs
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.5
occ:1.00
 O C:HOH950 2.0 24.1 1.0
OD1 C:ASP564 2.1 28.1 1.0
O C:HOH968 2.1 28.0 1.0
O C:HOH955 2.1 24.3 1.0
O C:HOH995 2.2 25.4 1.0
O C:HOH936 2.2 24.4 1.0
CG C:ASP564 3.1 27.8 1.0
OD2 C:ASP564 3.5 31.4 1.0
ZN C:ZN801 3.8 33.3 1.0
OE2 C:GLU592 4.0 31.8 1.0
O C:HOH923 4.0 34.4 1.0
NE2 C:HIS595 4.0 30.4 1.0
CD2 C:HIS567 4.1 30.5 1.0
O C:HIS563 4.2 28.6 1.0
CD2 C:HIS563 4.3 20.2 1.0
O C:HOH984 4.3 31.5 1.0
CD2 C:HIS595 4.4 35.0 1.0
OG1 C:THR633 4.4 25.4 1.0
NE2 C:HIS567 4.4 36.0 1.0
CB C:ASP564 4.4 26.1 1.0
O C:HOH1025 4.5 60.0 1.0
OD2 C:ASP674 4.6 35.5 1.0
CD2 C:HIS525 4.6 33.6 1.0
O C:THR633 4.7 29.5 1.0
NE2 C:HIS563 4.7 25.5 1.0
CB C:THR633 4.7 27.1 1.0
NE2 C:HIS525 4.7 35.4 1.0
CA C:ASP564 4.7 29.2 1.0
CD C:GLU592 4.8 31.8 1.0
CG C:GLU592 4.8 30.9 1.0
CE1 C:HIS595 5.0 31.9 1.0

Magnesium binding site 4 out of 4 in 5shs

Go back to Magnesium Binding Sites List in 5shs
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine


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 3- (Naphthalen-1-Ylmethyl)-7-Piperidin-1-Yltriazolo[4,5-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:37.9
occ:1.00
 O D:HOH950 2.0 26.7 1.0
OD1 D:ASP564 2.0 44.2 1.0
O D:HOH944 2.1 31.1 1.0
O D:HOH931 2.2 32.2 1.0
O D:HOH901 2.2 41.3 1.0
O D:HOH934 2.3 30.1 1.0
CG D:ASP564 2.9 35.2 1.0
OD2 D:ASP564 3.1 41.0 1.0
NE2 D:HIS595 3.8 37.6 1.0
O D:HOH926 3.9 44.6 1.0
ZN D:ZN801 3.9 43.4 1.0
CD2 D:HIS567 4.1 40.2 1.0
O D:HOH956 4.1 45.5 1.0
OE2 D:GLU592 4.2 36.6 1.0
CD2 D:HIS595 4.2 41.3 1.0
OG1 D:THR633 4.2 38.0 1.0
CB D:ASP564 4.3 35.6 1.0
O D:HIS563 4.3 39.0 1.0
NE2 D:HIS567 4.3 41.5 1.0
CD2 D:HIS563 4.3 30.5 1.0
CD2 D:HIS525 4.4 48.6 1.0
NE2 D:HIS525 4.6 41.8 1.0
CA D:ASP564 4.6 37.3 1.0
O D:THR633 4.7 39.2 1.0
NE2 D:HIS563 4.8 29.3 1.0
OD2 D:ASP674 4.8 35.6 1.0
CG D:GLU592 4.8 44.7 1.0
CB D:THR633 4.8 40.8 1.0
CD D:GLU592 4.9 37.1 1.0
CE1 D:HIS595 4.9 42.8 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 04:03:11 2024

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