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Magnesium in PDB 5sdx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine, PDB code: 5sdx 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) 43.68 / 2.19
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.377, 135.377, 235.362, 90, 90, 120
R / Rfree (%) 18.7 / 24.3

Other elements in 5sdx:

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

Magnesium binding site 1 out of 4 in 5sdx

Go back to Magnesium Binding Sites List in 5sdx
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


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 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:30.7
occ:1.00
 O A:HOH981 1.9 29.4 1.0
O A:HOH943 2.0 28.5 1.0
O A:HOH956 2.0 25.7 1.0
OD1 A:ASP564 2.0 29.8 1.0
O A:HOH904 2.0 30.1 1.0
O A:HOH926 2.1 33.7 1.0
CG A:ASP564 3.0 31.7 1.0
OD2 A:ASP564 3.4 33.1 1.0
ZN A:ZN801 3.8 36.9 1.0
O A:HOH970 3.8 32.0 1.0
OE2 A:GLU592 4.0 35.8 1.0
NE2 A:HIS595 4.1 29.9 1.0
O A:HOH931 4.1 44.5 1.0
OG1 A:THR633 4.2 37.8 1.0
CD2 A:HIS567 4.2 35.9 1.0
CD2 A:HIS563 4.4 31.6 1.0
NE2 A:HIS567 4.4 36.1 1.0
CB A:ASP564 4.4 32.0 1.0
CD2 A:HIS595 4.4 29.1 1.0
O A:HIS563 4.5 31.5 1.0
O A:THR633 4.5 33.8 1.0
OD2 A:ASP674 4.6 44.4 1.0
NE2 A:HIS525 4.6 34.9 1.0
CD2 A:HIS525 4.7 37.8 1.0
NE2 A:HIS563 4.7 29.0 1.0
CB A:THR633 4.8 30.8 1.0
CA A:ASP564 4.8 34.1 1.0
CG A:GLU592 4.8 35.4 1.0
CD A:GLU592 4.8 36.6 1.0
O A:HOH960 4.9 47.1 1.0

Magnesium binding site 2 out of 4 in 5sdx

Go back to Magnesium Binding Sites List in 5sdx
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


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 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:25.4
occ:1.00
 O B:HOH930 1.9 25.3 1.0
O B:HOH943 2.0 23.0 1.0
O B:HOH973 2.0 25.8 1.0
O B:HOH944 2.0 24.6 1.0
OD1 B:ASP564 2.1 28.1 1.0
O B:HOH903 2.1 23.8 1.0
CG B:ASP564 3.1 29.8 1.0
OD2 B:ASP564 3.5 34.7 1.0
O B:HOH986 3.7 51.1 1.0
O B:HOH970 3.8 29.3 1.0
ZN B:ZN801 3.8 35.2 1.0
OE2 B:GLU592 3.9 39.1 1.0
NE2 B:HIS595 4.0 30.8 1.0
CD2 B:HIS563 4.2 25.9 1.0
OG1 B:THR633 4.3 28.8 1.0
CD2 B:HIS595 4.3 33.9 1.0
CD2 B:HIS567 4.3 29.6 1.0
O B:HIS563 4.3 29.4 1.0
OD2 B:ASP674 4.4 34.1 1.0
NE2 B:HIS567 4.4 33.1 1.0
O B:HOH961 4.4 36.9 1.0
O B:THR633 4.4 30.3 1.0
CB B:ASP564 4.4 27.5 1.0
NE2 B:HIS563 4.5 28.4 1.0
CD2 B:HIS525 4.6 32.2 1.0
NE2 B:HIS525 4.6 29.1 1.0
CB B:THR633 4.7 30.3 1.0
CA B:ASP564 4.8 29.4 1.0
CD B:GLU592 4.8 33.8 1.0
CG B:GLU592 4.9 34.0 1.0

Magnesium binding site 3 out of 4 in 5sdx

Go back to Magnesium Binding Sites List in 5sdx
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


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 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.9
occ:1.00
 OD1 C:ASP564 2.0 31.7 1.0
O C:HOH950 2.0 29.8 1.0
O C:HOH980 2.0 29.9 1.0
O C:HOH924 2.1 33.0 1.0
O C:HOH952 2.2 29.3 1.0
O C:HOH929 2.2 25.5 1.0
CG C:ASP564 3.0 30.9 1.0
OD2 C:ASP564 3.3 32.3 1.0
ZN C:ZN801 3.8 37.2 1.0
NE2 C:HIS595 3.9 33.3 1.0
O C:HOH973 4.0 36.0 1.0
OE2 C:GLU592 4.1 37.6 1.0
CD2 C:HIS567 4.1 30.3 1.0
CD2 C:HIS563 4.2 29.1 1.0
NE2 C:HIS567 4.3 32.9 1.0
CD2 C:HIS595 4.3 35.6 1.0
O C:HIS563 4.3 31.2 1.0
OG1 C:THR633 4.3 32.5 1.0
O C:HOH957 4.3 41.2 1.0
CB C:ASP564 4.4 26.6 1.0
OD2 C:ASP674 4.4 38.0 1.0
CD2 C:HIS525 4.6 35.8 1.0
NE2 C:HIS525 4.6 34.6 1.0
O C:THR633 4.6 35.5 1.0
NE2 C:HIS563 4.6 34.7 1.0
CA C:ASP564 4.7 29.0 1.0
CB C:THR633 4.7 34.7 1.0
CG C:GLU592 4.9 34.8 1.0
CD C:GLU592 4.9 35.9 1.0

Magnesium binding site 4 out of 4 in 5sdx

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine


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 4-[6- [2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Pyridin-2-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:44.0
occ:1.00
 O D:HOH941 2.0 39.7 1.0
O D:HOH948 2.0 38.2 1.0
O D:HOH926 2.0 37.5 1.0
O D:HOH925 2.1 28.9 1.0
O D:HOH916 2.1 37.1 1.0
OD1 D:ASP564 2.1 39.7 1.0
CG D:ASP564 3.1 37.2 1.0
OD2 D:ASP564 3.4 45.6 1.0
O D:HOH945 3.7 39.3 1.0
ZN D:ZN801 3.8 45.7 1.0
OE2 D:GLU592 4.1 38.8 1.0
NE2 D:HIS595 4.2 48.8 1.0
CD2 D:HIS567 4.3 44.4 1.0
CD2 D:HIS563 4.3 39.4 1.0
OG1 D:THR633 4.3 40.7 1.0
O D:HIS563 4.4 37.3 1.0
OD2 D:ASP674 4.4 42.2 1.0
CB D:ASP564 4.5 37.1 1.0
CD2 D:HIS595 4.5 54.0 1.0
NE2 D:HIS567 4.5 40.3 1.0
CD2 D:HIS525 4.6 44.5 1.0
NE2 D:HIS525 4.6 45.6 1.0
O D:THR633 4.7 44.4 1.0
NE2 D:HIS563 4.7 34.3 1.0
CB D:THR633 4.7 42.8 1.0
CA D:ASP564 4.8 36.7 1.0
O D:HOH954 4.8 41.1 1.0
CD D:GLU592 4.9 45.6 1.0
CG D:GLU592 4.9 49.1 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 03:16:28 2024

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