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Zinc 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:

Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total 4 binding sites of Zinc 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 Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sg5

Go back to Zinc Binding Sites List in 5sg5
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:39.4
occ:1.00
 OD2 A:ASP564 2.0 35.8 1.0
NE2 A:HIS563 2.1 34.3 1.0
NE2 A:HIS529 2.2 34.7 1.0
OD1 A:ASP674 2.2 42.7 1.0
O A:HOH958 2.3 31.6 1.0
O A:HOH972 2.3 42.2 1.0
CD2 A:HIS563 3.0 33.9 1.0
CG A:ASP674 3.1 40.1 1.0
CE1 A:HIS529 3.1 35.7 1.0
CG A:ASP564 3.1 34.9 1.0
CD2 A:HIS529 3.2 34.8 1.0
CE1 A:HIS563 3.2 35.1 1.0
OD2 A:ASP674 3.3 48.6 1.0
OD1 A:ASP564 3.6 33.0 1.0
MG A:MG802 3.9 33.5 1.0
O A:HOH955 4.1 42.7 1.0
O A:HOH983 4.1 31.0 1.0
CG A:HIS563 4.2 32.6 1.0
ND1 A:HIS529 4.2 34.7 1.0
CD2 A:HIS525 4.2 40.9 1.0
ND1 A:HIS563 4.2 34.0 1.0
CG A:HIS529 4.3 34.2 1.0
CB A:ASP564 4.3 33.8 1.0
CB A:ASP674 4.4 37.0 1.0
NE2 A:HIS525 4.6 40.6 1.0
O A:HOH937 4.6 36.0 1.0
CG2 A:VAL533 4.7 32.5 1.0
O A:ASP674 4.8 34.8 1.0
CA A:ASP674 4.9 32.9 1.0

Zinc binding site 2 out of 4 in 5sg5

Go back to Zinc Binding Sites List in 5sg5
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:38.3
occ:1.00
 NE2 B:HIS563 2.1 32.5 1.0
OD2 B:ASP564 2.1 35.5 1.0
O B:HOH939 2.2 28.4 1.0
NE2 B:HIS529 2.2 33.4 1.0
OD1 B:ASP674 2.2 35.6 1.0
O B:HOH931 2.3 35.8 1.0
CD2 B:HIS563 3.0 32.2 1.0
CG B:ASP674 3.1 36.6 1.0
CG B:ASP564 3.1 30.9 1.0
CE1 B:HIS563 3.1 33.1 1.0
CD2 B:HIS529 3.1 36.5 1.0
CE1 B:HIS529 3.2 35.9 1.0
OD2 B:ASP674 3.3 39.7 1.0
OD1 B:ASP564 3.5 32.0 1.0
MG B:MG802 3.8 30.6 1.0
O B:HOH977 3.9 32.2 1.0
O B:HOH956 4.0 46.0 1.0
CD2 B:HIS525 4.1 36.7 1.0
CG B:HIS563 4.2 31.4 1.0
ND1 B:HIS563 4.2 32.5 1.0
CG B:HIS529 4.3 33.3 1.0
ND1 B:HIS529 4.3 35.9 1.0
CB B:ASP564 4.3 32.2 1.0
NE2 B:HIS525 4.4 36.0 1.0
CB B:ASP674 4.5 36.4 1.0
O B:HOH930 4.6 32.7 1.0
CG2 B:VAL533 4.8 29.2 1.0
CA B:ASP674 4.9 35.5 1.0
O B:ASP674 4.9 34.2 1.0

Zinc binding site 3 out of 4 in 5sg5

Go back to Zinc Binding Sites List in 5sg5
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:41.6
occ:1.00
 O C:HOH945 2.1 33.8 1.0
NE2 C:HIS563 2.1 34.0 1.0
OD2 C:ASP564 2.1 37.8 1.0
NE2 C:HIS529 2.2 37.9 1.0
OD1 C:ASP674 2.2 36.3 1.0
O C:HOH954 2.4 45.1 1.0
CD2 C:HIS563 3.0 32.5 1.0
CD2 C:HIS529 3.0 36.3 1.0
CG C:ASP674 3.1 36.9 1.0
CG C:ASP564 3.1 35.6 1.0
CE1 C:HIS563 3.2 37.6 1.0
CE1 C:HIS529 3.2 40.6 1.0
OD2 C:ASP674 3.3 40.6 1.0
OD1 C:ASP564 3.6 36.8 1.0
MG C:MG802 3.9 39.5 1.0
CD2 C:HIS525 4.1 44.5 1.0
CG C:HIS563 4.2 32.6 1.0
O C:HOH970 4.2 33.9 1.0
ND1 C:HIS563 4.2 31.9 1.0
CG C:HIS529 4.2 38.4 1.0
O C:HOH961 4.2 48.0 1.0
CB C:ASP564 4.3 33.0 1.0
ND1 C:HIS529 4.3 38.0 1.0
CB C:ASP674 4.4 40.7 1.0
NE2 C:HIS525 4.5 48.9 1.0
O C:HOH924 4.5 36.2 1.0
CG2 C:VAL533 4.8 33.1 1.0
CA C:ASP674 4.8 38.4 1.0
O C:ASP674 4.9 40.5 1.0

Zinc binding site 4 out of 4 in 5sg5

Go back to Zinc Binding Sites List in 5sg5
Zinc 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 Zinc with other atoms in the Zn 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:Zn801

b:53.5
occ:1.00
 O D:HOH915 2.1 39.3 1.0
NE2 D:HIS563 2.1 42.4 1.0
OD2 D:ASP564 2.1 59.2 1.0
NE2 D:HIS529 2.2 50.9 1.0
OD1 D:ASP674 2.2 49.5 1.0
O D:HOH920 2.4 41.2 1.0
CD2 D:HIS563 3.0 43.9 1.0
CG D:ASP564 3.1 45.8 1.0
CD2 D:HIS529 3.1 53.3 1.0
CG D:ASP674 3.2 50.3 1.0
CE1 D:HIS529 3.2 52.7 1.0
CE1 D:HIS563 3.2 45.4 1.0
OD2 D:ASP674 3.4 50.7 1.0
OD1 D:ASP564 3.6 44.2 1.0
MG D:MG802 3.8 47.8 1.0
O D:HOH919 3.9 53.3 1.0
O D:HOH931 4.1 44.6 1.0
CD2 D:HIS525 4.2 49.9 1.0
CG D:HIS563 4.2 44.2 1.0
CB D:ASP564 4.2 45.5 1.0
ND1 D:HIS563 4.3 44.5 1.0
CG D:HIS529 4.3 49.9 1.0
ND1 D:HIS529 4.3 50.1 1.0
NE2 D:HIS525 4.5 49.6 1.0
CB D:ASP674 4.5 51.6 1.0
O D:HOH907 4.6 49.3 1.0
CG2 D:VAL533 4.7 50.8 1.0
O D:ASP674 4.7 53.8 1.0
CA D:ASP674 4.9 49.2 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 Oct 28 05:08:14 2024

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