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Magnesium in PDB 5sdu: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole, PDB code: 5sdu 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) 43.75 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.21, 135.21, 235.801, 90, 90, 120
R / Rfree (%) 19.3 / 23.5

Other elements in 5sdu:

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

Magnesium binding site 1 out of 4 in 5sdu

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:22.1
occ:1.00
 O A:HOH1008 1.9 15.6 1.0
OD1 A:ASP564 2.0 18.5 1.0
O A:HOH959 2.0 18.8 1.0
O A:HOH944 2.1 19.9 1.0
O A:HOH920 2.1 21.7 1.0
O A:HOH969 2.2 19.6 1.0
CG A:ASP564 3.0 19.9 1.0
OD2 A:ASP564 3.4 21.5 1.0
ZN A:ZN801 3.8 24.7 1.0
O A:HOH1000 3.9 24.5 1.0
OE2 A:GLU592 4.0 24.8 1.0
NE2 A:HIS595 4.1 22.2 1.0
CD2 A:HIS567 4.3 21.9 1.0
O A:HOH1013 4.3 31.0 1.0
OG1 A:THR633 4.3 22.8 1.0
CD2 A:HIS563 4.3 18.6 1.0
CD2 A:HIS595 4.3 21.6 1.0
CB A:ASP564 4.4 19.0 1.0
O A:HIS563 4.4 20.3 1.0
NE2 A:HIS567 4.5 21.9 1.0
OD2 A:ASP674 4.5 30.1 1.0
O A:THR633 4.5 25.2 1.0
CD2 A:HIS525 4.6 24.4 1.0
NE2 A:HIS525 4.6 23.0 1.0
NE2 A:HIS563 4.7 18.2 1.0
CA A:ASP564 4.7 19.8 1.0
CB A:THR633 4.8 22.6 1.0
CD A:GLU592 4.8 24.4 1.0
CG A:GLU592 4.8 23.0 1.0

Magnesium binding site 2 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:16.2
occ:1.00
 O B:HOH919 1.8 18.3 1.0
O B:HOH923 2.0 13.5 1.0
O B:HOH942 2.0 14.8 1.0
O B:HOH1007 2.0 17.2 1.0
O B:HOH958 2.1 12.6 1.0
OD1 B:ASP564 2.1 18.2 1.0
CG B:ASP564 3.2 18.2 1.0
OD2 B:ASP564 3.5 18.8 1.0
O B:HOH1010 3.5 53.3 1.0
ZN B:ZN801 3.9 24.6 1.0
OE2 B:GLU592 3.9 21.2 1.0
NE2 B:HIS595 4.0 20.4 1.0
O B:HOH984 4.1 21.6 1.0
CD2 B:HIS563 4.2 16.5 1.0
OG1 B:THR633 4.3 19.8 1.0
OD2 B:ASP674 4.3 23.1 1.0
CD2 B:HIS595 4.3 21.4 1.0
O B:HIS563 4.3 21.6 1.0
CD2 B:HIS567 4.3 21.1 1.0
O B:HOH974 4.4 20.1 1.0
NE2 B:HIS567 4.5 21.1 1.0
O B:THR633 4.5 18.7 1.0
CB B:ASP564 4.5 18.3 1.0
NE2 B:HIS563 4.6 15.5 1.0
CB B:THR633 4.6 20.0 1.0
CD2 B:HIS525 4.6 22.1 1.0
CG B:GLU592 4.7 21.0 1.0
NE2 B:HIS525 4.7 21.9 1.0
CD B:GLU592 4.7 21.4 1.0
CA B:ASP564 4.8 18.9 1.0

Magnesium binding site 3 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:20.5
occ:1.00
 O C:HOH976 2.0 19.6 1.0
O C:HOH939 2.0 20.2 1.0
O C:HOH986 2.0 18.6 1.0
O C:HOH979 2.1 17.3 1.0
O C:HOH1027 2.1 16.4 1.0
OD1 C:ASP564 2.2 19.8 1.0
CG C:ASP564 3.1 19.3 1.0
OD2 C:ASP564 3.5 19.1 1.0
O C:HOH1044 3.5 44.5 1.0
ZN C:ZN801 3.8 26.8 1.0
O C:HOH1016 3.9 25.0 1.0
OE2 C:GLU592 4.1 25.7 1.0
NE2 C:HIS595 4.1 22.4 1.0
CD2 C:HIS563 4.2 18.5 1.0
CD2 C:HIS567 4.2 21.9 1.0
OG1 C:THR633 4.3 22.9 1.0
OD2 C:ASP674 4.3 28.6 1.0
O C:HIS563 4.3 17.8 1.0
NE2 C:HIS567 4.4 22.8 1.0
CD2 C:HIS595 4.4 22.6 1.0
O C:HOH989 4.4 30.5 1.0
CB C:ASP564 4.5 18.2 1.0
O C:THR633 4.5 21.8 1.0
NE2 C:HIS563 4.6 17.5 1.0
CB C:THR633 4.7 23.8 1.0
CD2 C:HIS525 4.7 22.9 1.0
NE2 C:HIS525 4.8 22.5 1.0
CG C:GLU592 4.8 23.3 1.0
CA C:ASP564 4.8 18.7 1.0
CD C:GLU592 4.9 24.2 1.0

Magnesium binding site 4 out of 4 in 5sdu

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


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 5- Methyl-4-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-2-Phenyl-1,3- Oxazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:31.2
occ:1.00
 O D:HOH981 2.1 25.6 1.0
O D:HOH975 2.1 26.4 1.0
O D:HOH925 2.1 19.8 1.0
O D:HOH915 2.1 30.5 1.0
OD1 D:ASP564 2.1 31.8 1.0
O D:HOH913 2.2 39.5 1.0
CG D:ASP564 3.1 32.6 1.0
OD2 D:ASP564 3.4 39.6 1.0
O D:HOH965 3.7 32.5 1.0
ZN D:ZN801 3.8 35.7 1.0
O D:HOH960 4.0 25.9 1.0
OE2 D:GLU592 4.0 35.0 1.0
NE2 D:HIS595 4.1 34.1 1.0
OG1 D:THR633 4.2 34.4 1.0
CD2 D:HIS567 4.2 36.9 1.0
CD2 D:HIS563 4.3 27.2 1.0
CD2 D:HIS595 4.4 33.8 1.0
O D:HIS563 4.4 28.1 1.0
CB D:ASP564 4.5 32.4 1.0
OD2 D:ASP674 4.5 33.9 1.0
NE2 D:HIS567 4.5 37.3 1.0
O D:THR633 4.5 33.8 1.0
CD2 D:HIS525 4.6 35.0 1.0
NE2 D:HIS525 4.7 36.6 1.0
NE2 D:HIS563 4.8 26.7 1.0
CB D:THR633 4.8 36.0 1.0
CA D:ASP564 4.8 30.6 1.0
CD D:GLU592 4.8 35.5 1.0
CG D:GLU592 4.9 34.8 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: Tue Aug 12 19:13:28 2025

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