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Magnesium in PDB 5sf9: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinoxaline

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinoxaline, PDB code: 5sf9 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) 43.78 / 2.37
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.64, 135.64, 235.889, 90, 90, 120
R / Rfree (%) 17.5 / 22.9

Other elements in 5sf9:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinoxaline (pdb code 5sf9). 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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinoxaline, PDB code: 5sf9:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sf9

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

b:44.0
occ:1.00
 O A:HOH946 1.9 41.8 1.0
O A:HOH925 2.0 44.9 1.0
O A:HOH926 2.0 51.0 1.0
O A:HOH910 2.0 37.2 1.0
O A:HOH929 2.1 41.4 1.0
OD1 A:ASP564 2.1 41.1 1.0
CG A:ASP564 3.2 44.8 1.0
OD2 A:ASP564 3.6 49.5 1.0
ZN A:ZN801 3.9 47.5 1.0
NE2 A:HIS595 4.0 40.6 1.0
OE2 A:GLU592 4.0 43.9 1.0
O A:HOH938 4.1 47.5 1.0
O A:HOH935 4.1 47.0 1.0
CD2 A:HIS567 4.2 46.6 1.0
O A:HIS563 4.3 41.1 1.0
CD2 A:HIS595 4.3 41.5 1.0
OG1 A:THR633 4.4 43.5 1.0
CD2 A:HIS563 4.4 38.6 1.0
CB A:ASP564 4.5 43.8 1.0
NE2 A:HIS567 4.5 48.1 1.0
OD2 A:ASP674 4.6 45.3 1.0
CD2 A:HIS525 4.6 45.4 1.0
O A:THR633 4.6 44.0 1.0
NE2 A:HIS525 4.7 46.7 1.0
NE2 A:HIS563 4.7 36.8 1.0
CA A:ASP564 4.8 42.7 1.0
CB A:THR633 4.8 45.7 1.0
CD A:GLU592 4.9 47.4 1.0
CG A:GLU592 4.9 43.0 1.0

Magnesium binding site 2 out of 4 in 5sf9

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

b:38.5
occ:1.00
 O B:HOH936 2.0 38.1 1.0
O B:HOH913 2.0 32.6 1.0
O B:HOH943 2.0 29.9 1.0
OD1 B:ASP564 2.0 43.9 1.0
O B:HOH919 2.0 40.6 1.0
O B:HOH911 2.2 31.7 1.0
CG B:ASP564 3.0 42.8 1.0
OD2 B:ASP564 3.4 41.5 1.0
ZN B:ZN801 3.8 44.5 1.0
O B:HOH944 4.0 46.9 1.0
NE2 B:HIS595 4.1 39.7 1.0
O B:HOH918 4.1 45.7 1.0
OE2 B:GLU592 4.1 38.9 1.0
CD2 B:HIS563 4.2 40.7 1.0
OG1 B:THR633 4.2 40.4 1.0
CD2 B:HIS567 4.2 43.9 1.0
O B:HIS563 4.3 45.5 1.0
CD2 B:HIS595 4.3 41.9 1.0
CB B:ASP564 4.3 41.2 1.0
OD2 B:ASP674 4.4 41.4 1.0
NE2 B:HIS567 4.5 48.2 1.0
NE2 B:HIS563 4.5 36.9 1.0
CD2 B:HIS525 4.6 48.1 1.0
O B:THR633 4.6 37.2 1.0
CA B:ASP564 4.7 44.5 1.0
CB B:THR633 4.7 42.1 1.0
NE2 B:HIS525 4.8 47.1 1.0
CG B:GLU592 4.8 44.6 1.0
CD B:GLU592 4.9 45.3 1.0

Magnesium binding site 3 out of 4 in 5sf9

Go back to Magnesium Binding Sites List in 5sf9
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-3-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]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-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Quinoxaline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:39.1
occ:1.00
 O C:HOH926 1.9 33.4 1.0
O C:HOH912 2.0 42.4 1.0
O C:HOH939 2.0 38.6 1.0
OD1 C:ASP564 2.1 40.3 1.0
O C:HOH954 2.1 34.2 1.0
O C:HOH916 2.2 32.3 1.0
CG C:ASP564 3.1 39.3 1.0
OD2 C:ASP564 3.4 42.8 1.0
ZN C:ZN801 3.8 43.6 1.0
O C:HOH928 4.0 42.9 1.0
O C:HOH933 4.0 44.0 1.0
NE2 C:HIS595 4.0 48.4 1.0
OE2 C:GLU592 4.1 43.9 1.0
CD2 C:HIS567 4.2 43.1 1.0
CD2 C:HIS563 4.2 36.4 1.0
CD2 C:HIS595 4.3 45.9 1.0
OG1 C:THR633 4.3 41.7 1.0
O C:HIS563 4.3 40.7 1.0
OD2 C:ASP674 4.4 41.8 1.0
CB C:ASP564 4.4 37.9 1.0
NE2 C:HIS567 4.4 41.8 1.0
O C:THR633 4.6 46.4 1.0
CB C:THR633 4.6 45.6 1.0
NE2 C:HIS563 4.7 36.8 1.0
CD2 C:HIS525 4.8 41.1 1.0
CA C:ASP564 4.8 38.6 1.0
NE2 C:HIS525 4.9 51.9 1.0
CG C:GLU592 4.9 43.6 1.0
CD C:GLU592 4.9 46.7 1.0

Magnesium binding site 4 out of 4 in 5sf9

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

b:57.1
occ:1.00
 O D:HOH907 1.9 53.0 1.0
O D:HOH909 1.9 53.4 1.0
O D:HOH904 2.0 57.8 1.0
O D:HOH905 2.1 42.9 1.0
OD1 D:ASP564 2.1 54.4 1.0
CG D:ASP564 3.1 55.3 1.0
OD2 D:ASP564 3.4 61.3 1.0
ZN D:ZN801 4.0 60.5 1.0
OE2 D:GLU592 4.0 66.1 1.0
CD2 D:HIS567 4.1 52.4 1.0
NE2 D:HIS595 4.1 63.6 1.0
O D:HOH910 4.1 53.6 1.0
NE2 D:HIS567 4.3 57.1 1.0
CD2 D:HIS595 4.3 62.6 1.0
OG1 D:THR633 4.4 62.6 1.0
CD2 D:HIS563 4.4 59.0 1.0
CB D:ASP564 4.4 56.7 1.0
O D:HIS563 4.4 60.0 1.0
CD2 D:HIS525 4.5 67.0 1.0
O D:THR633 4.5 57.1 1.0
NE2 D:HIS525 4.6 68.9 1.0
CA D:ASP564 4.7 55.3 1.0
NE2 D:HIS563 4.7 54.4 1.0
OD2 D:ASP674 4.8 68.7 1.0
CD D:GLU592 4.8 60.9 1.0
CB D:THR633 4.9 60.0 1.0
CG D:GLU592 4.9 60.5 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 03:30:55 2024

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