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Magnesium in PDB 5sg5: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea, PDB code: 5sg5 was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.56 / 2.17
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.423, 135.423, 235.489, 90, 90, 120
R / Rfree (%) 18.5 / 22.9

Other elements in 5sg5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea 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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea (pdb code 5sg5). 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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea, PDB code: 5sg5:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sg5

Go back to Magnesium Binding Sites List in 5sg5
Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea


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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:33.5
occ:1.00
 O A:HOH958 2.0 31.6 1.0
O A:HOH983 2.0 31.0 1.0
O A:HOH937 2.0 36.0 1.0
OD1 A:ASP564 2.0 33.0 1.0
O A:HOH963 2.1 31.9 1.0
O A:HOH907 2.2 35.1 1.0
CG A:ASP564 3.0 34.9 1.0
OD2 A:ASP564 3.4 35.8 1.0
ZN A:ZN801 3.9 39.4 1.0
O A:HOH972 4.0 42.2 1.0
OE2 A:GLU592 4.0 48.0 1.0
NE2 A:HIS595 4.0 37.3 1.0
O A:HOH967 4.2 46.2 1.0
OG1 A:THR633 4.3 38.2 1.0
O A:HIS563 4.3 32.8 1.0
CD2 A:HIS567 4.3 37.5 1.0
CD2 A:HIS563 4.3 33.9 1.0
CD2 A:HIS595 4.3 35.2 1.0
CB A:ASP564 4.4 33.8 1.0
O A:THR633 4.5 38.7 1.0
OD2 A:ASP674 4.5 48.6 1.0
NE2 A:HIS567 4.6 35.7 1.0
NE2 A:HIS563 4.7 34.3 1.0
CB A:THR633 4.7 35.9 1.0
CA A:ASP564 4.8 35.1 1.0
CG A:GLU592 4.8 38.2 1.0
CD2 A:HIS525 4.8 40.9 1.0
CD A:GLU592 4.8 41.1 1.0
NE2 A:HIS525 4.8 40.6 1.0

Magnesium binding site 2 out of 4 in 5sg5

Go back to Magnesium Binding Sites List in 5sg5
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea


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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:30.6
occ:1.00
 O B:HOH939 1.9 28.4 1.0
O B:HOH930 1.9 32.7 1.0
O B:HOH977 2.0 32.2 1.0
O B:HOH945 2.0 31.6 1.0
OD1 B:ASP564 2.1 32.0 1.0
O B:HOH910 2.1 25.7 1.0
CG B:ASP564 3.1 30.9 1.0
OD2 B:ASP564 3.5 35.5 1.0
ZN B:ZN801 3.8 38.3 1.0
OE2 B:GLU592 4.0 35.4 1.0
NE2 B:HIS595 4.0 34.6 1.0
O B:HOH931 4.0 35.8 1.0
CD2 B:HIS567 4.2 33.3 1.0
CD2 B:HIS563 4.3 32.2 1.0
CD2 B:HIS595 4.3 40.2 1.0
O B:HOH940 4.3 34.7 1.0
O B:HIS563 4.3 35.4 1.0
OG1 B:THR633 4.3 34.3 1.0
NE2 B:HIS567 4.3 33.6 1.0
OD2 B:ASP674 4.4 39.7 1.0
CB B:ASP564 4.4 32.2 1.0
O B:THR633 4.5 35.4 1.0
NE2 B:HIS563 4.6 32.5 1.0
CD2 B:HIS525 4.6 36.7 1.0
CB B:THR633 4.7 36.3 1.0
NE2 B:HIS525 4.7 36.0 1.0
CG B:GLU592 4.8 38.1 1.0
CD B:GLU592 4.8 38.4 1.0
CA B:ASP564 4.8 33.0 1.0

Magnesium binding site 3 out of 4 in 5sg5

Go back to Magnesium Binding Sites List in 5sg5
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea


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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:39.5
occ:1.00
 O C:HOH924 2.0 36.2 1.0
O C:HOH970 2.0 33.9 1.0
OD1 C:ASP564 2.1 36.8 1.0
O C:HOH945 2.1 33.8 1.0
O C:HOH947 2.1 34.8 1.0
O C:HOH940 2.1 29.8 1.0
CG C:ASP564 3.1 35.6 1.0
OD2 C:ASP564 3.5 37.8 1.0
ZN C:ZN801 3.9 41.6 1.0
OE2 C:GLU592 4.0 39.0 1.0
NE2 C:HIS595 4.0 38.8 1.0
O C:HOH954 4.0 45.1 1.0
O C:HOH933 4.0 47.0 1.0
CD2 C:HIS567 4.1 39.1 1.0
NE2 C:HIS567 4.2 38.7 1.0
CD2 C:HIS563 4.3 32.5 1.0
CD2 C:HIS595 4.3 38.4 1.0
O C:HIS563 4.3 35.9 1.0
OG1 C:THR633 4.4 37.6 1.0
CB C:ASP564 4.5 33.0 1.0
OD2 C:ASP674 4.5 40.6 1.0
O C:THR633 4.6 43.0 1.0
CD2 C:HIS525 4.6 44.5 1.0
NE2 C:HIS563 4.7 34.0 1.0
NE2 C:HIS525 4.7 48.9 1.0
CA C:ASP564 4.8 34.9 1.0
CD C:GLU592 4.8 36.8 1.0
CG C:GLU592 4.9 34.7 1.0
CB C:THR633 4.9 37.7 1.0

Magnesium binding site 4 out of 4 in 5sg5

Go back to Magnesium Binding Sites List in 5sg5
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea


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 1-[(4- Methoxyphenyl)Methyl]-3-(4-Methylphenyl)-1-[(4-Oxo-3H-Quinazolin-2- Yl)Methyl]Urea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:47.8
occ:1.00
 O D:HOH931 2.0 44.6 1.0
O D:HOH927 2.1 33.5 1.0
O D:HOH917 2.1 50.1 1.0
O D:HOH915 2.1 39.3 1.0
O D:HOH907 2.1 49.3 1.0
OD1 D:ASP564 2.2 44.2 1.0
CG D:ASP564 3.2 45.8 1.0
OD2 D:ASP564 3.5 59.2 1.0
ZN D:ZN801 3.8 53.5 1.0
O D:HOH920 3.9 41.2 1.0
O D:HOH925 3.9 45.5 1.0
OE2 D:GLU592 4.1 55.8 1.0
NE2 D:HIS595 4.1 54.7 1.0
OG1 D:THR633 4.3 50.7 1.0
CD2 D:HIS567 4.3 55.9 1.0
CD2 D:HIS563 4.3 43.9 1.0
CD2 D:HIS595 4.4 52.1 1.0
O D:HIS563 4.4 43.7 1.0
O D:THR633 4.4 57.5 1.0
OD2 D:ASP674 4.4 50.7 1.0
CB D:ASP564 4.5 45.5 1.0
NE2 D:HIS567 4.5 55.3 1.0
CD2 D:HIS525 4.7 49.9 1.0
NE2 D:HIS525 4.7 49.6 1.0
NE2 D:HIS563 4.8 42.4 1.0
CB D:THR633 4.8 49.2 1.0
CA D:ASP564 4.8 43.9 1.0
CG D:GLU592 4.9 54.2 1.0
CD D:GLU592 4.9 56.2 1.0

Reference:

A.Flohr, D.Schlatter, B.Kuhn, M.G.Rudolph. Crystal Structure of A Human Phosphodiesterase 10 Complex To Be Published.
Page generated: Mon Sep 30 03:43:42 2024

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