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Magnesium in PDB 5sjg: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One, PDB code: 5sjg 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) 43.58 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.482, 135.482, 235.361, 90, 90, 120
R / Rfree (%) 17.6 / 22.4

Other elements in 5sjg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One 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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One (pdb code 5sjg). 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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One, PDB code: 5sjg:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjg

Go back to Magnesium Binding Sites List in 5sjg
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:24.4
occ:1.00
 O A:HOH1010 1.9 19.4 1.0
O A:HOH923 2.0 22.0 1.0
OD1 A:ASP564 2.0 24.1 1.0
O A:HOH983 2.1 25.0 1.0
O A:HOH970 2.1 23.0 1.0
O A:HOH915 2.2 20.3 1.0
CG A:ASP564 3.0 23.0 1.0
OD2 A:ASP564 3.4 26.6 1.0
O A:HOH982 3.8 40.0 1.0
ZN A:ZN801 3.9 28.4 1.0
OE2 A:GLU592 3.9 26.1 1.0
NE2 A:HIS595 4.0 23.2 1.0
CD2 A:HIS567 4.2 25.2 1.0
OG1 A:THR633 4.3 26.4 1.0
O A:HOH995 4.3 31.6 1.0
O A:HIS563 4.3 23.2 1.0
CB A:ASP564 4.4 23.9 1.0
CD2 A:HIS595 4.4 20.6 1.0
NE2 A:HIS567 4.4 23.6 1.0
O A:THR633 4.5 27.2 1.0
CD2 A:HIS563 4.5 21.2 1.0
CD2 A:HIS525 4.5 28.5 1.0
OD2 A:ASP674 4.6 29.2 1.0
NE2 A:HIS525 4.6 27.9 1.0
CA A:ASP564 4.7 23.4 1.0
CD A:GLU592 4.8 27.8 1.0
CB A:THR633 4.8 25.7 1.0
CG A:GLU592 4.8 26.2 1.0
NE2 A:HIS563 4.8 21.6 1.0
CE1 A:HIS595 5.0 20.2 1.0

Magnesium binding site 2 out of 4 in 5sjg

Go back to Magnesium Binding Sites List in 5sjg
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.6
occ:1.00
 O B:HOH974 2.0 19.8 1.0
O B:HOH915 2.0 22.0 1.0
OD1 B:ASP564 2.1 22.0 1.0
O B:HOH931 2.1 20.9 1.0
O B:HOH983 2.1 18.8 1.0
O B:HOH1002 2.2 21.5 1.0
CG B:ASP564 3.1 21.4 1.0
OD2 B:ASP564 3.5 21.5 1.0
ZN B:ZN801 3.8 26.8 1.0
NE2 B:HIS595 4.0 21.2 1.0
OE2 B:GLU592 4.0 26.6 1.0
O B:HOH962 4.0 45.6 1.0
OG1 B:THR633 4.2 23.3 1.0
O B:HOH1058 4.2 38.1 1.0
CD2 B:HIS563 4.2 22.1 1.0
CD2 B:HIS567 4.3 21.8 1.0
O B:HIS563 4.3 24.0 1.0
CD2 B:HIS595 4.3 23.1 1.0
O B:HOH978 4.3 25.4 1.0
CB B:ASP564 4.5 20.8 1.0
NE2 B:HIS567 4.5 21.3 1.0
OD2 B:ASP674 4.5 24.3 1.0
CD2 B:HIS525 4.5 24.7 1.0
NE2 B:HIS563 4.6 20.8 1.0
O B:THR633 4.6 25.6 1.0
CB B:THR633 4.7 24.4 1.0
NE2 B:HIS525 4.7 28.1 1.0
CG B:GLU592 4.7 26.7 1.0
CA B:ASP564 4.7 22.2 1.0
CD B:GLU592 4.8 25.7 1.0

Magnesium binding site 3 out of 4 in 5sjg

Go back to Magnesium Binding Sites List in 5sjg
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:22.9
occ:1.00
 O C:HOH1016 2.0 20.6 1.0
O C:HOH961 2.0 27.7 1.0
O C:HOH978 2.0 21.9 1.0
O C:HOH970 2.1 21.8 1.0
OD1 C:ASP564 2.1 21.7 1.0
O C:HOH936 2.2 20.4 1.0
CG C:ASP564 3.1 23.9 1.0
OD2 C:ASP564 3.5 25.2 1.0
ZN C:ZN801 3.8 28.2 1.0
OE2 C:GLU592 3.9 26.1 1.0
O C:HOH972 4.0 36.5 1.0
NE2 C:HIS595 4.0 25.8 1.0
O C:HOH1046 4.2 47.6 1.0
OG1 C:THR633 4.2 23.1 1.0
CD2 C:HIS567 4.2 23.9 1.0
O C:HIS563 4.3 23.3 1.0
O C:HOH1003 4.3 27.3 1.0
CD2 C:HIS563 4.4 20.9 1.0
CD2 C:HIS595 4.4 26.2 1.0
NE2 C:HIS567 4.5 23.7 1.0
CB C:ASP564 4.5 22.1 1.0
OD2 C:ASP674 4.5 32.1 1.0
O C:THR633 4.5 28.1 1.0
CD2 C:HIS525 4.5 26.4 1.0
NE2 C:HIS525 4.5 27.2 1.0
CB C:THR633 4.8 25.5 1.0
NE2 C:HIS563 4.8 21.4 1.0
CG C:GLU592 4.8 22.7 1.0
CA C:ASP564 4.8 22.0 1.0
CD C:GLU592 4.8 24.3 1.0

Magnesium binding site 4 out of 4 in 5sjg

Go back to Magnesium Binding Sites List in 5sjg
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.1
occ:1.00
 O D:HOH951 2.0 22.6 1.0
O D:HOH938 2.0 29.9 1.0
O D:HOH974 2.1 24.0 1.0
O D:HOH969 2.1 26.1 1.0
OD1 D:ASP564 2.1 30.8 1.0
O D:HOH919 2.2 28.0 1.0
CG D:ASP564 3.1 30.5 1.0
OD2 D:ASP564 3.4 36.8 1.0
O D:HOH947 3.6 39.2 1.0
ZN D:ZN801 3.7 32.9 1.0
O D:HOH978 4.1 32.7 1.0
OE2 D:GLU592 4.1 35.7 1.0
NE2 D:HIS595 4.1 32.0 1.0
OG1 D:THR633 4.2 30.8 1.0
CD2 D:HIS563 4.3 26.8 1.0
CD2 D:HIS567 4.3 33.6 1.0
O D:HIS563 4.4 28.2 1.0
CD2 D:HIS595 4.4 32.2 1.0
OD2 D:ASP674 4.4 32.1 1.0
CB D:ASP564 4.4 30.8 1.0
O D:THR633 4.5 33.5 1.0
CD2 D:HIS525 4.5 32.2 1.0
NE2 D:HIS525 4.5 37.8 1.0
NE2 D:HIS567 4.6 30.3 1.0
NE2 D:HIS563 4.6 24.1 1.0
CB D:THR633 4.7 31.7 1.0
CA D:ASP564 4.9 29.9 1.0
CD D:GLU592 4.9 35.7 1.0
CG D:GLU592 5.0 36.6 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 04:21:22 2024

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