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Magnesium in PDB 5se9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine, PDB code: 5se9 was solved by C.Joseph, K.Groebke-Zbinden, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.74 / 1.94
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.599, 135.599, 235.637, 90, 90, 120
R / Rfree (%) 17.5 / 21.9

Other elements in 5se9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine (pdb code 5se9). 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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine, PDB code: 5se9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se9

Go back to Magnesium Binding Sites List in 5se9
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.4
occ:1.00
 O A:HOH1034 1.9 26.4 1.0
O A:HOH1005 2.0 24.1 1.0
OD1 A:ASP564 2.0 25.5 1.0
O A:HOH931 2.0 23.7 1.0
O A:HOH954 2.1 25.6 1.0
O A:HOH942 2.1 22.9 1.0
CG A:ASP564 3.1 27.8 1.0
OD2 A:ASP564 3.4 26.8 1.0
ZN A:ZN801 3.8 31.2 1.0
O A:HOH1050 3.8 40.9 1.0
O A:HOH984 3.9 30.5 1.0
OE2 A:GLU592 4.0 28.6 1.0
NE2 A:HIS595 4.1 27.1 1.0
OG1 A:THR633 4.2 25.3 1.0
O A:HOH1009 4.3 30.1 1.0
CD2 A:HIS567 4.3 29.6 1.0
O A:HIS563 4.4 24.5 1.0
CD2 A:HIS595 4.4 25.3 1.0
CD2 A:HIS563 4.4 23.6 1.0
CB A:ASP564 4.4 26.7 1.0
O A:THR633 4.5 26.1 1.0
NE2 A:HIS567 4.5 26.8 1.0
OD2 A:ASP674 4.6 29.9 1.0
NE2 A:HIS525 4.6 29.6 1.0
CD2 A:HIS525 4.7 27.8 1.0
CB A:THR633 4.7 27.9 1.0
NE2 A:HIS563 4.8 27.5 1.0
CA A:ASP564 4.8 27.2 1.0
CG A:GLU592 4.8 28.6 1.0
CD A:GLU592 4.8 28.4 1.0

Magnesium binding site 2 out of 4 in 5se9

Go back to Magnesium Binding Sites List in 5se9
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:23.9
occ:1.00
 O B:HOH946 2.0 23.8 1.0
O B:HOH959 2.0 20.6 1.0
O B:HOH953 2.1 23.2 1.0
OD1 B:ASP564 2.1 23.0 1.0
O B:HOH1018 2.1 22.4 1.0
O B:HOH979 2.1 21.2 1.0
CG B:ASP564 3.1 22.7 1.0
OD2 B:ASP564 3.5 22.8 1.0
ZN B:ZN801 3.8 29.8 1.0
O B:HOH1067 3.9 41.0 1.0
NE2 B:HIS595 4.0 23.5 1.0
OE2 B:GLU592 4.0 26.6 1.0
O B:HOH1012 4.1 29.5 1.0
OG1 B:THR633 4.1 25.0 1.0
CD2 B:HIS563 4.3 22.7 1.0
O B:HOH981 4.3 26.0 1.0
CD2 B:HIS567 4.3 25.9 1.0
O B:HIS563 4.3 26.4 1.0
CD2 B:HIS595 4.3 23.6 1.0
NE2 B:HIS567 4.5 23.4 1.0
CB B:ASP564 4.5 21.9 1.0
OD2 B:ASP674 4.5 24.5 1.0
O B:THR633 4.6 24.0 1.0
CD2 B:HIS525 4.6 26.2 1.0
NE2 B:HIS563 4.6 23.0 1.0
NE2 B:HIS525 4.6 28.3 1.0
CB B:THR633 4.6 24.8 1.0
CA B:ASP564 4.8 21.9 1.0
CG B:GLU592 4.8 24.9 1.0
CD B:GLU592 4.9 22.6 1.0

Magnesium binding site 3 out of 4 in 5se9

Go back to Magnesium Binding Sites List in 5se9
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.5
occ:1.00
 O C:HOH953 2.0 24.9 1.0
O C:HOH1050 2.0 25.6 1.0
OD1 C:ASP564 2.1 22.5 1.0
O C:HOH984 2.1 23.5 1.0
O C:HOH958 2.1 22.8 1.0
O C:HOH937 2.2 25.3 1.0
CG C:ASP564 3.1 25.7 1.0
OD2 C:ASP564 3.5 24.7 1.0
ZN C:ZN801 3.8 30.6 1.0
O C:HOH1064 3.9 42.7 1.0
OE2 C:GLU592 3.9 28.3 1.0
NE2 C:HIS595 4.0 25.9 1.0
O C:HOH1006 4.1 28.4 1.0
OG1 C:THR633 4.2 24.8 1.0
CD2 C:HIS567 4.2 26.8 1.0
O C:HOH1015 4.2 31.7 1.0
CD2 C:HIS595 4.3 24.2 1.0
CD2 C:HIS563 4.3 22.1 1.0
O C:HIS563 4.3 25.6 1.0
OD2 C:ASP674 4.4 31.3 1.0
CB C:ASP564 4.4 22.1 1.0
NE2 C:HIS567 4.5 25.4 1.0
O C:THR633 4.5 28.3 1.0
CD2 C:HIS525 4.6 28.2 1.0
CB C:THR633 4.7 27.6 1.0
NE2 C:HIS525 4.7 28.3 1.0
NE2 C:HIS563 4.7 22.7 1.0
CA C:ASP564 4.8 25.8 1.0
CD C:GLU592 4.8 27.1 1.0
CG C:GLU592 4.8 24.1 1.0

Magnesium binding site 4 out of 4 in 5se9

Go back to Magnesium Binding Sites List in 5se9
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:34.6
occ:1.00
 O D:HOH937 2.0 26.9 1.0
O D:HOH963 2.1 28.2 1.0
O D:HOH906 2.1 30.3 1.0
O D:HOH961 2.2 28.8 1.0
O D:HOH915 2.2 33.4 1.0
OD1 D:ASP564 2.2 34.1 1.0
CG D:ASP564 3.2 29.3 1.0
OD2 D:ASP564 3.6 35.0 1.0
ZN D:ZN801 3.7 37.4 1.0
O D:HOH974 3.8 36.5 1.0
OE2 D:GLU592 3.9 34.5 1.0
O D:HOH993 4.0 37.9 1.0
NE2 D:HIS595 4.1 34.6 1.0
OG1 D:THR633 4.2 34.0 1.0
CD2 D:HIS567 4.3 35.3 1.0
CD2 D:HIS563 4.3 34.5 1.0
OD2 D:ASP674 4.4 35.6 1.0
CD2 D:HIS595 4.4 36.4 1.0
O D:THR633 4.4 36.6 1.0
O D:HIS563 4.5 33.5 1.0
NE2 D:HIS567 4.5 33.3 1.0
NE2 D:HIS525 4.5 41.0 1.0
CD2 D:HIS525 4.6 35.2 1.0
CB D:ASP564 4.6 30.0 1.0
CB D:THR633 4.6 34.1 1.0
NE2 D:HIS563 4.8 29.6 1.0
CD D:GLU592 4.8 40.4 1.0
CG D:GLU592 4.9 39.8 1.0
CA D:ASP564 4.9 30.4 1.0
O D:HOH999 4.9 35.8 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Sep 30 03:20:01 2024

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