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

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]Quinoxaline, PDB code: 5sek 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) 43.63 / 2.15
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.629, 135.629, 236.677, 90, 90, 120
R / Rfree (%) 16.4 / 19.7

Other elements in 5sek:

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

Magnesium binding site 1 out of 4 in 5sek

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


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

b:27.1
occ:1.00
 OD1 A:ASP564 1.9 27.5 1.0
O A:HOH999 2.0 26.6 1.0
O A:HOH929 2.0 28.9 1.0
O A:HOH942 2.1 29.8 1.0
O A:HOH969 2.1 29.1 1.0
O A:HOH940 2.1 27.7 1.0
CG A:ASP564 2.9 28.7 1.0
OD2 A:ASP564 3.3 29.1 1.0
ZN A:ZN801 3.8 33.8 1.0
O A:HOH1010 3.9 34.8 1.0
NE2 A:HIS595 4.0 30.4 1.0
O A:HOH1037 4.0 48.1 1.0
OE2 A:GLU592 4.0 33.3 1.0
CD2 A:HIS595 4.2 31.7 1.0
CD2 A:HIS567 4.2 30.3 1.0
CB A:ASP564 4.3 27.5 1.0
OG1 A:THR633 4.3 28.4 1.0
CD2 A:HIS563 4.3 26.8 1.0
O A:HIS563 4.3 30.5 1.0
O A:HOH1003 4.4 37.6 1.0
NE2 A:HIS567 4.5 29.5 1.0
CD2 A:HIS525 4.5 29.0 1.0
O A:THR633 4.6 31.4 1.0
OD2 A:ASP674 4.6 34.1 1.0
NE2 A:HIS525 4.6 29.5 1.0
NE2 A:HIS563 4.6 27.3 1.0
CA A:ASP564 4.6 27.4 1.0
CB A:THR633 4.8 28.0 1.0
CG A:GLU592 4.8 31.0 1.0
CD A:GLU592 4.9 32.5 1.0

Magnesium binding site 2 out of 4 in 5sek

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


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

b:23.1
occ:1.00
 O B:HOH934 2.0 24.7 1.0
O B:HOH930 2.0 27.4 1.0
O B:HOH938 2.1 26.2 1.0
O B:HOH959 2.2 23.2 1.0
O B:HOH995 2.2 28.6 1.0
OD1 B:ASP564 2.2 25.2 1.0
CG B:ASP564 3.2 24.8 1.0
OD2 B:ASP564 3.6 24.1 1.0
O B:HOH1041 3.6 50.1 1.0
OE2 B:GLU592 3.8 29.6 1.0
ZN B:ZN801 3.9 33.2 1.0
NE2 B:HIS595 4.0 31.6 1.0
O B:HOH1002 4.1 37.7 1.0
OG1 B:THR633 4.1 25.5 1.0
CD2 B:HIS563 4.2 26.7 1.0
CD2 B:HIS595 4.2 31.1 1.0
O B:HIS563 4.2 26.4 1.0
CD2 B:HIS567 4.3 27.4 1.0
O B:HOH958 4.3 30.2 1.0
OD2 B:ASP674 4.4 27.9 1.0
O B:THR633 4.4 27.9 1.0
NE2 B:HIS567 4.4 26.9 1.0
CB B:ASP564 4.5 26.0 1.0
NE2 B:HIS563 4.6 25.7 1.0
CB B:THR633 4.6 26.9 1.0
CD2 B:HIS525 4.6 27.9 1.0
CD B:GLU592 4.7 28.9 1.0
NE2 B:HIS525 4.7 28.4 1.0
CG B:GLU592 4.7 29.3 1.0
CA B:ASP564 4.8 26.5 1.0

Magnesium binding site 3 out of 4 in 5sek

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


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

b:27.3
occ:1.00
 O C:HOH967 2.0 25.9 1.0
O C:HOH945 2.0 32.5 1.0
OD1 C:ASP564 2.1 27.2 1.0
O C:HOH1013 2.1 28.1 1.0
O C:HOH926 2.2 25.1 1.0
O C:HOH994 2.3 30.3 1.0
CG C:ASP564 3.0 26.6 1.0
OD2 C:ASP564 3.4 25.9 1.0
ZN C:ZN801 3.8 33.5 1.0
OE2 C:GLU592 4.0 33.9 1.0
O C:HOH1010 4.0 44.5 1.0
O C:HOH1035 4.1 41.8 1.0
NE2 C:HIS595 4.1 29.1 1.0
CD2 C:HIS563 4.2 26.3 1.0
CD2 C:HIS567 4.3 29.6 1.0
CD2 C:HIS595 4.3 29.4 1.0
O C:HIS563 4.3 29.4 1.0
OG1 C:THR633 4.3 32.9 1.0
OD2 C:ASP674 4.4 31.8 1.0
CB C:ASP564 4.4 26.6 1.0
O C:HOH1008 4.5 35.1 1.0
NE2 C:HIS567 4.5 28.6 1.0
O C:THR633 4.5 29.3 1.0
NE2 C:HIS563 4.6 26.3 1.0
CB C:THR633 4.6 29.7 1.0
CD2 C:HIS525 4.7 29.6 1.0
NE2 C:HIS525 4.7 29.5 1.0
CA C:ASP564 4.8 27.7 1.0
CD C:GLU592 4.8 32.1 1.0
CG C:GLU592 4.9 30.8 1.0

Magnesium binding site 4 out of 4 in 5sek

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


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

b:34.4
occ:1.00
 O D:HOH976 2.1 34.5 1.0
O D:HOH907 2.1 38.1 1.0
O D:HOH925 2.1 28.9 1.0
O D:HOH906 2.2 32.4 1.0
O D:HOH971 2.3 30.8 1.0
OD1 D:ASP564 2.3 39.0 1.0
CG D:ASP564 3.3 38.4 1.0
OD2 D:ASP564 3.6 38.5 1.0
O D:HOH973 3.8 46.2 1.0
ZN D:ZN801 3.9 39.6 1.0
OE2 D:GLU592 3.9 40.7 1.0
O D:HOH977 4.1 44.0 1.0
NE2 D:HIS595 4.2 42.5 1.0
O D:THR633 4.3 46.0 1.0
OD2 D:ASP674 4.3 37.0 1.0
OG1 D:THR633 4.3 43.7 1.0
CD2 D:HIS567 4.3 42.6 1.0
CD2 D:HIS595 4.4 41.9 1.0
NE2 D:HIS567 4.5 41.4 1.0
CD2 D:HIS563 4.5 33.6 1.0
O D:HIS563 4.5 37.4 1.0
CD2 D:HIS525 4.6 37.4 1.0
CB D:ASP564 4.6 37.8 1.0
NE2 D:HIS525 4.7 40.3 1.0
CB D:THR633 4.7 43.1 1.0
O D:HOH982 4.8 35.4 1.0
CD D:GLU592 4.8 41.5 1.0
NE2 D:HIS563 4.8 32.8 1.0
CG D:GLU592 4.9 41.1 1.0
C D:THR633 5.0 42.5 1.0
CA D:ASP564 5.0 38.5 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 03:23:11 2024

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