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Magnesium in PDB 5sf5: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine

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

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine, PDB code: 5sf5 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) 43.82 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.992, 135.992, 236.077, 90, 90, 120
R / Rfree (%) 17.8 / 22.3

Other elements in 5sf5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine (pdb code 5sf5). 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-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine, PDB code: 5sf5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sf5

Go back to Magnesium Binding Sites List in 5sf5
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:26.8
occ:1.00
 O A:HOH1026 1.9 26.1 1.0
OD1 A:ASP564 2.0 26.5 1.0
O A:HOH931 2.0 22.9 1.0
O A:HOH945 2.1 26.2 1.0
O A:HOH974 2.2 26.5 1.0
O A:HOH935 2.2 26.0 1.0
CG A:ASP564 3.0 32.3 1.0
OD2 A:ASP564 3.4 29.8 1.0
ZN A:ZN801 3.8 32.8 1.0
O A:HOH987 3.9 29.1 1.0
OE2 A:GLU592 4.0 29.1 1.0
NE2 A:HIS595 4.1 25.3 1.0
OG1 A:THR633 4.1 28.8 1.0
O A:HOH1049 4.1 40.8 1.0
O A:HOH1015 4.3 31.5 1.0
CD2 A:HIS563 4.3 23.8 1.0
CD2 A:HIS595 4.4 24.1 1.0
O A:HIS563 4.4 29.4 1.0
CB A:ASP564 4.4 29.6 1.0
CD2 A:HIS567 4.4 27.3 1.0
O A:THR633 4.5 31.2 1.0
OD2 A:ASP674 4.5 34.6 1.0
NE2 A:HIS567 4.6 27.3 1.0
CB A:THR633 4.6 29.6 1.0
CD2 A:HIS525 4.7 31.4 1.0
NE2 A:HIS525 4.7 30.9 1.0
CA A:ASP564 4.8 27.9 1.0
NE2 A:HIS563 4.8 25.7 1.0
CG A:GLU592 4.8 27.6 1.0
CD A:GLU592 4.9 27.8 1.0

Magnesium binding site 2 out of 4 in 5sf5

Go back to Magnesium Binding Sites List in 5sf5
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.5
occ:1.00
 O B:HOH942 2.0 28.2 1.0
O B:HOH969 2.0 20.6 1.0
O B:HOH912 2.1 23.5 1.0
OD1 B:ASP564 2.1 25.5 1.0
O B:HOH1015 2.1 24.0 1.0
O B:HOH991 2.1 20.7 1.0
CG B:ASP564 3.1 26.3 1.0
OD2 B:ASP564 3.4 26.3 1.0
ZN B:ZN801 3.8 31.6 1.0
OE2 B:GLU592 3.9 33.5 1.0
NE2 B:HIS595 4.0 24.6 1.0
O B:HOH981 4.0 32.1 1.0
O B:HOH1061 4.0 37.6 1.0
OG1 B:THR633 4.2 25.0 1.0
CD2 B:HIS563 4.2 24.6 1.0
O B:HIS563 4.3 28.8 1.0
CD2 B:HIS567 4.3 30.1 1.0
O B:HOH947 4.3 25.8 1.0
CD2 B:HIS595 4.3 28.9 1.0
CB B:ASP564 4.4 24.6 1.0
OD2 B:ASP674 4.5 24.8 1.0
NE2 B:HIS567 4.5 25.3 1.0
NE2 B:HIS563 4.6 25.4 1.0
O B:THR633 4.6 25.9 1.0
NE2 B:HIS525 4.6 29.8 1.0
CD2 B:HIS525 4.6 26.8 1.0
CB B:THR633 4.6 25.1 1.0
CG B:GLU592 4.7 27.5 1.0
CA B:ASP564 4.8 27.5 1.0
CD B:GLU592 4.8 28.0 1.0

Magnesium binding site 3 out of 4 in 5sf5

Go back to Magnesium Binding Sites List in 5sf5
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.0
occ:1.00
 OD1 C:ASP564 2.0 25.5 1.0
O C:HOH946 2.0 24.4 1.0
O C:HOH966 2.0 26.8 1.0
O C:HOH985 2.1 25.8 1.0
O C:HOH945 2.2 26.6 1.0
O C:HOH1024 2.2 26.0 1.0
CG C:ASP564 3.0 24.3 1.0
OD2 C:ASP564 3.4 24.8 1.0
ZN C:ZN801 3.8 32.8 1.0
OE2 C:GLU592 4.0 29.3 1.0
O C:HOH968 4.0 35.5 1.0
NE2 C:HIS595 4.1 29.0 1.0
O C:HOH1062 4.1 42.5 1.0
CD2 C:HIS563 4.2 27.8 1.0
OG1 C:THR633 4.2 29.1 1.0
CD2 C:HIS567 4.3 27.9 1.0
O C:HIS563 4.3 26.6 1.0
CD2 C:HIS595 4.3 26.6 1.0
O C:HOH971 4.4 32.6 1.0
CB C:ASP564 4.4 23.6 1.0
OD2 C:ASP674 4.4 33.0 1.0
O C:THR633 4.5 29.7 1.0
NE2 C:HIS567 4.5 29.1 1.0
NE2 C:HIS563 4.6 27.6 1.0
CD2 C:HIS525 4.6 29.6 1.0
NE2 C:HIS525 4.7 29.8 1.0
CB C:THR633 4.7 28.9 1.0
CA C:ASP564 4.7 27.4 1.0
CG C:GLU592 4.9 29.5 1.0
CD C:GLU592 4.9 27.1 1.0

Magnesium binding site 4 out of 4 in 5sf5

Go back to Magnesium Binding Sites List in 5sf5
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,3- Dimethyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]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-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Imidazo[1,2- B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:37.8
occ:1.00
 O D:HOH953 2.0 29.6 1.0
O D:HOH967 2.1 30.4 1.0
O D:HOH905 2.1 36.9 1.0
OD1 D:ASP564 2.1 37.2 1.0
O D:HOH907 2.1 31.3 1.0
O D:HOH976 2.2 32.7 1.0
CG D:ASP564 3.1 34.2 1.0
OD2 D:ASP564 3.5 38.9 1.0
ZN D:ZN801 3.8 39.1 1.0
O D:HOH982 3.8 33.6 1.0
OE2 D:GLU592 4.0 37.1 1.0
NE2 D:HIS595 4.0 37.5 1.0
OG1 D:THR633 4.1 34.9 1.0
O D:HOH987 4.1 39.7 1.0
CD2 D:HIS595 4.3 37.2 1.0
CD2 D:HIS563 4.3 27.6 1.0
O D:HIS563 4.4 36.3 1.0
CD2 D:HIS567 4.4 36.6 1.0
OD2 D:ASP674 4.4 41.7 1.0
O D:THR633 4.4 41.0 1.0
CB D:ASP564 4.5 34.5 1.0
CB D:THR633 4.6 37.9 1.0
NE2 D:HIS567 4.6 35.5 1.0
CD2 D:HIS525 4.7 37.4 1.0
NE2 D:HIS525 4.7 44.9 1.0
CA D:ASP564 4.8 32.6 1.0
CG D:GLU592 4.8 39.0 1.0
CD D:GLU592 4.8 40.2 1.0
NE2 D:HIS563 4.9 26.2 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 03:30:12 2024

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