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Magnesium in PDB 5shq: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine, PDB code: 5shq 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) 34.92 / 2.08
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.136, 135.136, 234.1, 90, 90, 120
R / Rfree (%) 18.2 / 22.2

Other elements in 5shq:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine (pdb code 5shq). 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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine, PDB code: 5shq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shq

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.2
occ:1.00
 O A:HOH1020 1.9 24.2 1.0
O A:HOH973 2.0 27.2 1.0
O A:HOH936 2.1 25.1 1.0
OD1 A:ASP564 2.1 26.1 1.0
O A:HOH967 2.2 24.7 1.0
O A:HOH959 2.2 29.4 1.0
CG A:ASP564 3.1 27.1 1.0
OD2 A:ASP564 3.4 28.7 1.0
ZN A:ZN801 3.8 31.4 1.0
OE2 A:GLU592 4.0 32.1 1.0
O A:HOH1005 4.0 32.9 1.0
NE2 A:HIS595 4.0 26.9 1.0
OG1 A:THR633 4.2 30.8 1.0
CD2 A:HIS567 4.3 33.0 1.0
CD2 A:HIS563 4.3 25.9 1.0
O A:HOH998 4.3 37.2 1.0
CD2 A:HIS595 4.3 28.4 1.0
O A:HIS563 4.4 28.4 1.0
CB A:ASP564 4.4 26.8 1.0
NE2 A:HIS567 4.5 34.3 1.0
O A:THR633 4.5 29.6 1.0
OD2 A:ASP674 4.5 37.6 1.0
CD2 A:HIS525 4.6 29.9 1.0
NE2 A:HIS563 4.6 26.5 1.0
CB A:THR633 4.7 28.9 1.0
NE2 A:HIS525 4.8 28.8 1.0
CA A:ASP564 4.8 27.3 1.0
CG A:GLU592 4.8 31.2 1.0
CD A:GLU592 4.8 32.5 1.0

Magnesium binding site 2 out of 4 in 5shq

Go back to Magnesium Binding Sites List in 5shq
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:26.8
occ:1.00
 O B:HOH945 1.9 25.7 1.0
O B:HOH937 1.9 22.2 1.0
O B:HOH986 2.0 20.9 1.0
O B:HOH1010 2.1 22.4 1.0
O B:HOH914 2.1 24.1 1.0
OD1 B:ASP564 2.1 27.1 1.0
CG B:ASP564 3.1 26.7 1.0
OD2 B:ASP564 3.5 27.7 1.0
ZN B:ZN801 3.8 30.3 1.0
OE2 B:GLU592 4.0 29.4 1.0
O B:HOH1024 4.0 43.0 1.0
NE2 B:HIS595 4.0 29.1 1.0
O B:HOH966 4.1 37.1 1.0
CD2 B:HIS563 4.2 25.5 1.0
CD2 B:HIS567 4.2 30.0 1.0
OG1 B:THR633 4.2 27.1 1.0
O B:HIS563 4.3 28.5 1.0
CD2 B:HIS595 4.3 30.4 1.0
OD2 B:ASP674 4.3 30.0 1.0
O B:HOH977 4.4 33.2 1.0
NE2 B:HIS567 4.4 29.5 1.0
CB B:ASP564 4.4 27.0 1.0
NE2 B:HIS563 4.5 26.7 1.0
O B:THR633 4.6 29.6 1.0
CD2 B:HIS525 4.7 28.8 1.0
CA B:ASP564 4.7 27.3 1.0
CB B:THR633 4.7 26.9 1.0
NE2 B:HIS525 4.8 31.0 1.0
CD B:GLU592 4.8 27.5 1.0
CG B:GLU592 4.8 28.6 1.0

Magnesium binding site 3 out of 4 in 5shq

Go back to Magnesium Binding Sites List in 5shq
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.2
occ:1.00
 O C:HOH950 2.0 28.3 1.0
O C:HOH1002 2.0 26.7 1.0
O C:HOH926 2.1 23.6 1.0
OD1 C:ASP564 2.1 25.8 1.0
O C:HOH1022 2.1 26.0 1.0
O C:HOH943 2.2 25.1 1.0
CG C:ASP564 3.1 25.9 1.0
OD2 C:ASP564 3.4 26.5 1.0
ZN C:ZN801 3.8 32.0 1.0
O C:HOH992 4.0 35.3 1.0
OE2 C:GLU592 4.0 32.6 1.0
NE2 C:HIS595 4.1 29.4 1.0
CD2 C:HIS563 4.2 27.0 1.0
OG1 C:THR633 4.2 30.5 1.0
CD2 C:HIS567 4.2 30.3 1.0
O C:HIS563 4.2 26.1 1.0
OD2 C:ASP674 4.3 34.1 1.0
O C:HOH979 4.3 33.8 1.0
CD2 C:HIS595 4.4 26.9 1.0
NE2 C:HIS567 4.4 29.9 1.0
CB C:ASP564 4.4 26.4 1.0
O C:THR633 4.5 30.0 1.0
NE2 C:HIS563 4.6 27.9 1.0
CB C:THR633 4.7 27.4 1.0
CA C:ASP564 4.7 27.3 1.0
CD2 C:HIS525 4.8 32.6 1.0
CG C:GLU592 4.8 29.8 1.0
NE2 C:HIS525 4.8 33.4 1.0
CD C:GLU592 4.9 33.4 1.0

Magnesium binding site 4 out of 4 in 5shq

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-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 4- Pyrrolidin-1-Yl-7H-Pyrrolo[2,3-D]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:39.4
occ:1.00
 O D:HOH977 2.0 34.3 1.0
O D:HOH931 2.1 39.8 1.0
O D:HOH961 2.1 30.9 1.0
OD1 D:ASP564 2.1 36.8 1.0
O D:HOH934 2.2 28.9 1.0
O D:HOH919 2.2 35.1 1.0
CG D:ASP564 3.2 35.2 1.0
OD2 D:ASP564 3.5 39.2 1.0
ZN D:ZN801 3.9 40.5 1.0
O D:HOH951 3.9 42.9 1.0
NE2 D:HIS595 4.0 40.1 1.0
O D:HOH970 4.0 40.5 1.0
OE2 D:GLU592 4.1 39.4 1.0
CD2 D:HIS567 4.1 44.0 1.0
OG1 D:THR633 4.2 39.5 1.0
CD2 D:HIS595 4.3 39.1 1.0
NE2 D:HIS567 4.3 40.9 1.0
CD2 D:HIS563 4.4 33.7 1.0
O D:HIS563 4.5 34.9 1.0
CB D:ASP564 4.5 35.7 1.0
OD2 D:ASP674 4.5 41.0 1.0
O D:THR633 4.6 42.4 1.0
CD2 D:HIS525 4.6 43.7 1.0
NE2 D:HIS525 4.7 45.8 1.0
CA D:ASP564 4.8 33.1 1.0
NE2 D:HIS563 4.8 32.1 1.0
CB D:THR633 4.8 39.9 1.0
CG D:GLU592 4.8 42.6 1.0
CD D:GLU592 4.9 41.7 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 04:02:50 2024

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