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Magnesium in PDB 5sh3: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine, PDB code: 5sh3 was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.64 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.337, 135.337, 235.108, 90, 90, 120
R / Rfree (%) 17.1 / 22.2

Other elements in 5sh3:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine 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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine (pdb code 5sh3). 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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine, PDB code: 5sh3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sh3

Go back to Magnesium Binding Sites List in 5sh3
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine


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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.8
occ:1.00
 O A:HOH1021 2.0 24.6 1.0
OD1 A:ASP564 2.0 26.2 1.0
O A:HOH947 2.0 21.9 1.0
O A:HOH989 2.1 24.8 1.0
O A:HOH963 2.1 23.5 1.0
O A:HOH923 2.2 21.5 1.0
CG A:ASP564 3.1 27.1 1.0
OD2 A:ASP564 3.4 26.2 1.0
ZN A:ZN801 3.8 29.9 1.0
O A:HOH988 3.9 33.0 1.0
OE2 A:GLU592 3.9 31.8 1.0
NE2 A:HIS595 4.0 24.5 1.0
CD2 A:HIS567 4.2 28.4 1.0
OG1 A:THR633 4.2 25.7 1.0
O A:HOH991 4.3 30.3 1.0
CD2 A:HIS563 4.3 25.9 1.0
O A:HIS563 4.4 26.3 1.0
CD2 A:HIS595 4.4 22.1 1.0
CB A:ASP564 4.4 26.3 1.0
NE2 A:HIS567 4.4 23.1 1.0
O A:THR633 4.6 26.7 1.0
NE2 A:HIS525 4.6 30.1 1.0
CD2 A:HIS525 4.6 32.0 1.0
OD2 A:ASP674 4.6 30.2 1.0
CB A:THR633 4.7 29.3 1.0
NE2 A:HIS563 4.7 26.0 1.0
CA A:ASP564 4.8 26.2 1.0
CD A:GLU592 4.8 29.6 1.0
CG A:GLU592 4.8 29.3 1.0

Magnesium binding site 2 out of 4 in 5sh3

Go back to Magnesium Binding Sites List in 5sh3
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine


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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.7
occ:1.00
 O B:HOH958 2.0 24.2 1.0
O B:HOH978 2.1 19.0 1.0
O B:HOH999 2.1 19.4 1.0
OD1 B:ASP564 2.1 23.8 1.0
O B:HOH1013 2.1 21.3 1.0
O B:HOH907 2.1 20.6 1.0
CG B:ASP564 3.1 23.1 1.0
OD2 B:ASP564 3.5 24.1 1.0
ZN B:ZN801 3.8 28.2 1.0
OE2 B:GLU592 4.0 26.2 1.0
NE2 B:HIS595 4.0 24.3 1.0
O B:HOH966 4.0 33.0 1.0
O B:HOH1067 4.0 45.0 1.0
OG1 B:THR633 4.1 24.1 1.0
O B:HIS563 4.2 24.9 1.0
CD2 B:HIS567 4.2 24.7 1.0
CD2 B:HIS563 4.3 22.6 1.0
O B:HOH954 4.3 26.7 1.0
CD2 B:HIS595 4.3 23.4 1.0
NE2 B:HIS567 4.4 23.6 1.0
CB B:ASP564 4.5 21.0 1.0
OD2 B:ASP674 4.5 23.6 1.0
NE2 B:HIS563 4.6 22.7 1.0
CD2 B:HIS525 4.6 23.1 1.0
O B:THR633 4.6 21.8 1.0
NE2 B:HIS525 4.6 28.5 1.0
CG B:GLU592 4.7 24.4 1.0
CB B:THR633 4.7 24.7 1.0
CA B:ASP564 4.7 21.7 1.0
CD B:GLU592 4.8 25.5 1.0

Magnesium binding site 3 out of 4 in 5sh3

Go back to Magnesium Binding Sites List in 5sh3
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine


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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.6
occ:1.00
 OD1 C:ASP564 2.0 23.7 1.0
O C:HOH1034 2.1 23.3 1.0
O C:HOH943 2.1 26.5 1.0
O C:HOH927 2.1 24.6 1.0
O C:HOH976 2.1 26.3 1.0
O C:HOH932 2.2 26.7 1.0
CG C:ASP564 3.0 25.0 1.0
OD2 C:ASP564 3.4 26.1 1.0
ZN C:ZN801 3.8 29.7 1.0
O C:HOH1045 3.9 41.4 1.0
O C:HOH1002 4.0 34.9 1.0
NE2 C:HIS595 4.0 24.8 1.0
OE2 C:GLU592 4.1 28.1 1.0
CD2 C:HIS567 4.2 24.1 1.0
OG1 C:THR633 4.2 25.6 1.0
CD2 C:HIS563 4.3 22.0 1.0
O C:HOH1004 4.3 27.2 1.0
O C:HIS563 4.3 24.9 1.0
OD2 C:ASP674 4.3 28.3 1.0
CD2 C:HIS595 4.4 24.9 1.0
CB C:ASP564 4.4 25.8 1.0
NE2 C:HIS567 4.5 26.2 1.0
CD2 C:HIS525 4.5 26.2 1.0
O C:THR633 4.5 29.0 1.0
NE2 C:HIS525 4.6 29.3 1.0
NE2 C:HIS563 4.7 23.8 1.0
CB C:THR633 4.7 25.8 1.0
CA C:ASP564 4.8 23.3 1.0
CG C:GLU592 4.8 28.1 1.0
CD C:GLU592 4.9 25.3 1.0

Magnesium binding site 4 out of 4 in 5sh3

Go back to Magnesium Binding Sites List in 5sh3
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine


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 2,3- Dimethyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]- 8-Methylsulfonylimidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:35.1
occ:1.00
 O D:HOH913 2.0 33.7 1.0
OD1 D:ASP564 2.1 31.3 1.0
O D:HOH942 2.1 25.1 1.0
O D:HOH970 2.1 27.8 1.0
O D:HOH964 2.1 27.2 1.0
O D:HOH916 2.2 24.0 1.0
CG D:ASP564 3.1 30.9 1.0
OD2 D:ASP564 3.5 33.2 1.0
ZN D:ZN801 3.8 35.9 1.0
O D:HOH951 3.9 32.7 1.0
OE2 D:GLU592 4.0 33.8 1.0
NE2 D:HIS595 4.0 32.3 1.0
OG1 D:THR633 4.1 31.0 1.0
CD2 D:HIS563 4.2 28.6 1.0
CD2 D:HIS595 4.3 29.8 1.0
O D:HOH959 4.3 36.5 1.0
CD2 D:HIS567 4.3 29.5 1.0
O D:HIS563 4.3 32.2 1.0
OD2 D:ASP674 4.5 32.1 1.0
CB D:ASP564 4.5 29.5 1.0
O D:THR633 4.6 36.8 1.0
CB D:THR633 4.6 29.3 1.0
NE2 D:HIS567 4.6 32.2 1.0
NE2 D:HIS525 4.6 39.5 1.0
NE2 D:HIS563 4.6 25.9 1.0
CD2 D:HIS525 4.6 33.8 1.0
CA D:ASP564 4.8 29.7 1.0
CD D:GLU592 4.9 38.2 1.0
CG D:GLU592 4.9 38.8 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 03:54:37 2024

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