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Magnesium in PDB 5sk3: Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sk3 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) 43.75 / 2.32
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.212, 135.212, 235.801, 90, 90, 120
R / Rfree (%) 16.9 / 22.6

Other elements in 5sk3:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol (pdb code 5sk3). 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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol, PDB code: 5sk3:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sk3

Go back to Magnesium Binding Sites List in 5sk3
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg803

b:36.1
occ:1.00
 O A:HOH972 1.9 29.4 1.0
OD1 A:ASP564 1.9 36.9 1.0
O A:HOH904 2.0 28.4 1.0
O A:HOH931 2.0 28.4 1.0
O A:HOH932 2.1 36.8 1.0
O A:HOH936 2.2 32.7 1.0
CG A:ASP564 2.9 35.8 1.0
OD2 A:ASP564 3.2 41.6 1.0
ZN A:ZN802 3.6 42.3 1.0
O A:HOH952 3.8 33.9 1.0
NE2 A:HIS595 4.1 31.1 1.0
OE2 A:GLU592 4.1 38.5 1.0
CD2 A:HIS563 4.2 34.6 1.0
O A:HOH945 4.2 39.2 1.0
OG1 A:THR633 4.3 37.8 1.0
CB A:ASP564 4.3 32.8 1.0
O A:HIS563 4.3 38.2 1.0
CD2 A:HIS567 4.4 39.1 1.0
CD2 A:HIS595 4.4 33.3 1.0
OD2 A:ASP674 4.5 45.3 1.0
NE2 A:HIS525 4.5 42.5 1.0
O A:THR633 4.5 38.1 1.0
CD2 A:HIS525 4.6 45.5 1.0
NE2 A:HIS563 4.6 30.7 1.0
CB A:THR633 4.6 37.0 1.0
NE2 A:HIS567 4.7 38.3 1.0
CA A:ASP564 4.7 38.0 1.0
CG A:GLU592 4.8 35.4 1.0
CD A:GLU592 4.9 38.9 1.0

Magnesium binding site 2 out of 4 in 5sk3

Go back to Magnesium Binding Sites List in 5sk3
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg803

b:37.6
occ:1.00
 O B:HOH934 1.9 33.8 1.0
O B:HOH952 1.9 27.8 1.0
O B:HOH974 2.0 25.0 1.0
OD1 B:ASP564 2.1 37.4 1.0
O B:HOH951 2.1 30.2 1.0
O B:HOH908 2.1 26.0 1.0
CG B:ASP564 3.1 32.8 1.0
OD2 B:ASP564 3.4 36.9 1.0
ZN B:ZN802 3.8 39.9 1.0
OE2 B:GLU592 3.9 31.8 1.0
NE2 B:HIS595 4.0 33.4 1.0
O B:HOH961 4.0 36.0 1.0
OG1 B:THR633 4.2 36.5 1.0
CD2 B:HIS563 4.2 34.7 1.0
O B:HOH955 4.2 34.5 1.0
CD2 B:HIS595 4.3 38.9 1.0
CD2 B:HIS567 4.3 36.3 1.0
O B:HIS563 4.4 36.6 1.0
NE2 B:HIS567 4.4 37.0 1.0
CB B:ASP564 4.4 34.6 1.0
OD2 B:ASP674 4.4 38.3 1.0
O B:THR633 4.5 35.8 1.0
NE2 B:HIS563 4.6 34.3 1.0
CB B:THR633 4.6 37.9 1.0
CD2 B:HIS525 4.6 37.5 1.0
CG B:GLU592 4.7 33.0 1.0
CD B:GLU592 4.7 37.1 1.0
NE2 B:HIS525 4.7 38.7 1.0
CA B:ASP564 4.8 36.9 1.0

Magnesium binding site 3 out of 4 in 5sk3

Go back to Magnesium Binding Sites List in 5sk3
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg803

b:36.6
occ:1.00
 OD1 C:ASP564 1.9 39.7 1.0
O C:HOH968 2.0 35.5 1.0
O C:HOH951 2.0 40.1 1.0
O C:HOH933 2.0 29.3 1.0
O C:HOH942 2.2 31.2 1.0
O C:HOH977 2.3 31.4 1.0
CG C:ASP564 2.9 38.1 1.0
OD2 C:ASP564 3.3 39.4 1.0
ZN C:ZN802 3.8 41.9 1.0
NE2 C:HIS595 3.9 41.8 1.0
O C:HOH989 4.0 51.5 1.0
O C:HOH964 4.0 35.5 1.0
OE2 C:GLU592 4.1 33.9 1.0
O C:HOH937 4.1 34.1 1.0
CD2 C:HIS567 4.1 33.0 1.0
CD2 C:HIS563 4.2 32.2 1.0
CD2 C:HIS595 4.2 43.3 1.0
O C:HIS563 4.3 33.5 1.0
CB C:ASP564 4.3 35.6 1.0
OG1 C:THR633 4.3 31.9 1.0
NE2 C:HIS567 4.4 36.7 1.0
OD2 C:ASP674 4.5 39.4 1.0
NE2 C:HIS563 4.5 34.8 1.0
O C:THR633 4.6 38.8 1.0
CD2 C:HIS525 4.6 40.3 1.0
CA C:ASP564 4.7 35.4 1.0
NE2 C:HIS525 4.7 44.0 1.0
CB C:THR633 4.7 39.3 1.0
CG C:GLU592 4.8 34.9 1.0
CD C:GLU592 4.9 36.1 1.0

Magnesium binding site 4 out of 4 in 5sk3

Go back to Magnesium Binding Sites List in 5sk3
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with [2- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol


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- Cyclopropyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazin-3-Yl]Methanol within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg803

b:50.5
occ:1.00
 O D:HOH927 2.0 44.6 1.0
O D:HOH923 2.0 46.2 1.0
OD1 D:ASP564 2.0 54.3 1.0
O D:HOH919 2.1 36.9 1.0
O D:HOH904 2.1 45.7 1.0
O D:HOH903 2.2 45.9 1.0
CG D:ASP564 3.0 56.9 1.0
OD2 D:ASP564 3.3 61.1 1.0
O D:HOH928 3.7 47.1 1.0
O D:HOH908 3.8 46.8 1.0
ZN D:ZN802 3.8 57.9 1.0
NE2 D:HIS595 3.9 61.6 1.0
OE2 D:GLU592 4.0 44.9 1.0
CD2 D:HIS567 4.1 51.4 1.0
O D:HIS563 4.2 55.0 1.0
CD2 D:HIS595 4.2 62.8 1.0
OG1 D:THR633 4.2 52.2 1.0
CD2 D:HIS563 4.3 45.8 1.0
CB D:ASP564 4.3 52.6 1.0
NE2 D:HIS567 4.4 54.8 1.0
CD2 D:HIS525 4.5 58.2 1.0
CA D:ASP564 4.6 50.8 1.0
O D:THR633 4.6 56.6 1.0
OD2 D:ASP674 4.7 71.3 1.0
NE2 D:HIS525 4.7 58.0 1.0
NE2 D:HIS563 4.8 44.5 1.0
CB D:THR633 4.8 58.2 1.0
CD D:GLU592 4.9 52.1 1.0
CE1 D:HIS595 5.0 58.3 1.0
CG D:GLU592 5.0 56.1 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 04:30:03 2024

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