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Magnesium in PDB 5se6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine, PDB code: 5se6 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) 43.50 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.828, 134.828, 234.402, 90, 90, 120
R / Rfree (%) 17.7 / 21.9

Other elements in 5se6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine 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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine (pdb code 5se6). 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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine, PDB code: 5se6:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5se6

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:25.1
occ:1.00
 O A:HOH1025 1.9 24.4 1.0
O A:HOH972 1.9 22.8 1.0
O A:HOH922 2.0 24.2 1.0
OD1 A:ASP564 2.0 25.0 1.0
O A:HOH964 2.1 21.0 1.0
O A:HOH926 2.2 25.5 1.0
CG A:ASP564 3.0 23.6 1.0
OD2 A:ASP564 3.3 28.1 1.0
ZN A:ZN801 3.7 30.1 1.0
O A:HOH1013 3.9 36.3 1.0
OE2 A:GLU592 4.0 30.1 1.0
NE2 A:HIS595 4.1 27.5 1.0
OG1 A:THR633 4.1 26.3 1.0
CD2 A:HIS563 4.3 23.9 1.0
O A:HOH990 4.3 31.5 1.0
CD2 A:HIS595 4.3 24.2 1.0
CB A:ASP564 4.4 23.6 1.0
CD2 A:HIS567 4.4 26.3 1.0
O A:HIS563 4.4 25.6 1.0
OD2 A:ASP674 4.4 30.9 1.0
O A:THR633 4.5 28.7 1.0
NE2 A:HIS567 4.5 24.2 1.0
NE2 A:HIS563 4.6 26.2 1.0
CD2 A:HIS525 4.7 30.5 1.0
CB A:THR633 4.7 25.5 1.0
NE2 A:HIS525 4.7 30.7 1.0
CA A:ASP564 4.8 25.2 1.0
CG A:GLU592 4.8 27.1 1.0
CD A:GLU592 4.8 27.9 1.0

Magnesium binding site 2 out of 4 in 5se6

Go back to Magnesium Binding Sites List in 5se6
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:22.1
occ:1.00
 O B:HOH974 1.9 19.8 1.0
O B:HOH947 1.9 21.6 1.0
O B:HOH1015 2.0 25.4 1.0
O B:HOH920 2.0 21.3 1.0
O B:HOH985 2.1 20.4 1.0
OD1 B:ASP564 2.1 24.1 1.0
CG B:ASP564 3.1 22.9 1.0
OD2 B:ASP564 3.5 23.1 1.0
ZN B:ZN801 3.8 29.6 1.0
O B:HOH987 4.0 35.7 1.0
OE2 B:GLU592 4.0 28.7 1.0
NE2 B:HIS595 4.0 24.0 1.0
OG1 B:THR633 4.1 23.3 1.0
CD2 B:HIS567 4.3 22.7 1.0
CD2 B:HIS563 4.3 23.1 1.0
CD2 B:HIS595 4.3 24.7 1.0
O B:HIS563 4.3 26.2 1.0
O B:HOH968 4.3 26.3 1.0
OD2 B:ASP674 4.4 27.9 1.0
NE2 B:HIS567 4.4 22.7 1.0
CB B:ASP564 4.5 23.7 1.0
O B:THR633 4.5 24.1 1.0
CD2 B:HIS525 4.6 26.5 1.0
CB B:THR633 4.6 26.4 1.0
NE2 B:HIS563 4.7 22.1 1.0
NE2 B:HIS525 4.7 28.8 1.0
CG B:GLU592 4.7 27.0 1.0
CA B:ASP564 4.8 22.1 1.0
CD B:GLU592 4.8 27.4 1.0

Magnesium binding site 3 out of 4 in 5se6

Go back to Magnesium Binding Sites List in 5se6
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:26.0
occ:1.00
 O C:HOH981 2.0 24.2 1.0
O C:HOH961 2.0 26.8 1.0
OD1 C:ASP564 2.0 23.7 1.0
O C:HOH1005 2.1 21.8 1.0
O C:HOH1037 2.1 25.5 1.0
O C:HOH933 2.2 21.3 1.0
CG C:ASP564 3.1 23.4 1.0
OD2 C:ASP564 3.4 24.1 1.0
ZN C:ZN801 3.8 31.4 1.0
O C:HOH969 4.0 39.0 1.0
OE2 C:GLU592 4.0 30.3 1.0
NE2 C:HIS595 4.0 25.5 1.0
O C:HOH1052 4.1 51.4 1.0
CD2 C:HIS567 4.1 28.0 1.0
OG1 C:THR633 4.2 27.0 1.0
CD2 C:HIS563 4.3 24.1 1.0
O C:HIS563 4.3 24.9 1.0
O C:HOH967 4.3 29.3 1.0
CD2 C:HIS595 4.3 24.4 1.0
NE2 C:HIS567 4.4 28.0 1.0
OD2 C:ASP674 4.4 35.8 1.0
CB C:ASP564 4.4 23.2 1.0
O C:THR633 4.5 26.3 1.0
NE2 C:HIS563 4.6 25.5 1.0
CD2 C:HIS525 4.7 32.0 1.0
CB C:THR633 4.7 27.7 1.0
CG C:GLU592 4.7 26.6 1.0
NE2 C:HIS525 4.7 31.0 1.0
CA C:ASP564 4.8 21.8 1.0
CD C:GLU592 4.8 26.9 1.0

Magnesium binding site 4 out of 4 in 5se6

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine


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 2,9- Dimethyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:30.5
occ:1.00
 O D:HOH991 2.0 28.4 1.0
O D:HOH998 2.0 32.1 1.0
O D:HOH947 2.0 25.9 1.0
O D:HOH939 2.1 26.8 1.0
O D:HOH919 2.1 30.6 1.0
OD1 D:ASP564 2.1 27.7 1.0
CG D:ASP564 3.1 26.9 1.0
OD2 D:ASP564 3.5 33.0 1.0
ZN D:ZN801 3.7 35.0 1.0
NE2 D:HIS595 4.0 33.0 1.0
OE2 D:GLU592 4.0 36.3 1.0
O D:HOH966 4.1 34.8 1.0
O D:HOH977 4.1 36.7 1.0
OG1 D:THR633 4.1 29.8 1.0
CD2 D:HIS595 4.2 32.4 1.0
CD2 D:HIS563 4.3 29.1 1.0
O D:HIS563 4.3 29.5 1.0
CD2 D:HIS567 4.3 38.5 1.0
OD2 D:ASP674 4.4 36.3 1.0
O D:THR633 4.4 33.7 1.0
CB D:ASP564 4.5 29.3 1.0
NE2 D:HIS567 4.5 33.9 1.0
CD2 D:HIS525 4.6 37.2 1.0
CB D:THR633 4.6 31.4 1.0
NE2 D:HIS563 4.7 25.9 1.0
NE2 D:HIS525 4.7 37.0 1.0
CA D:ASP564 4.8 27.8 1.0
CG D:GLU592 4.8 36.0 1.0
CD D:GLU592 4.9 40.3 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: Tue Aug 12 19:16:53 2025

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