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Zinc in PDB 5sig: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea, PDB code: 5sig 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) 43.42 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.988, 134.988, 235.078, 90, 90, 120
R / Rfree (%) 18.7 / 22.3

Other elements in 5sig:

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

Zinc binding site 1 out of 4 in 5sig

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea


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]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.2
occ:1.00
 OD2 A:ASP564 2.0 27.3 1.0
O A:HOH931 2.1 26.2 1.0
NE2 A:HIS563 2.1 27.4 1.0
NE2 A:HIS529 2.1 28.4 1.0
OD1 A:ASP674 2.2 31.4 1.0
O A:HOH961 2.5 38.3 1.0
CD2 A:HIS563 3.0 26.6 1.0
CG A:ASP564 3.0 27.6 1.0
CG A:ASP674 3.1 32.4 1.0
CD2 A:HIS529 3.1 30.2 1.0
CE1 A:HIS529 3.1 28.5 1.0
CE1 A:HIS563 3.2 27.9 1.0
OD2 A:ASP674 3.3 36.4 1.0
OD1 A:ASP564 3.6 28.5 1.0
MG A:MG802 3.8 27.5 1.0
CD2 A:HIS525 4.1 32.9 1.0
O A:HOH1002 4.1 24.9 1.0
O A:HOH990 4.2 39.4 1.0
CG A:HIS563 4.2 27.5 1.0
ND1 A:HIS529 4.2 27.9 1.0
ND1 A:HIS563 4.2 27.6 1.0
CG A:HIS529 4.2 28.0 1.0
CB A:ASP564 4.2 27.4 1.0
NE2 A:HIS525 4.5 34.6 1.0
CB A:ASP674 4.5 30.3 1.0
O A:HOH963 4.7 24.3 1.0
CG2 A:VAL533 4.8 27.0 1.0
O A:ASP674 4.9 27.6 1.0
CA A:ASP674 4.9 29.0 1.0

Zinc binding site 2 out of 4 in 5sig

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea


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]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.0
occ:1.00
 O B:HOH934 2.0 23.2 1.0
NE2 B:HIS563 2.1 24.3 1.0
NE2 B:HIS529 2.1 27.5 1.0
OD1 B:ASP674 2.2 27.1 1.0
OD2 B:ASP564 2.2 27.5 1.0
O B:HOH986 2.3 38.3 1.0
CG B:ASP674 3.0 29.0 1.0
CD2 B:HIS563 3.1 25.1 1.0
CD2 B:HIS529 3.1 28.5 1.0
CG B:ASP564 3.1 26.1 1.0
CE1 B:HIS563 3.1 26.0 1.0
CE1 B:HIS529 3.1 26.6 1.0
OD2 B:ASP674 3.3 31.0 1.0
OD1 B:ASP564 3.6 27.4 1.0
MG B:MG802 3.7 24.1 1.0
O B:HOH1008 4.0 28.2 1.0
O B:HOH949 4.1 38.6 1.0
CD2 B:HIS525 4.1 33.5 1.0
CG B:HIS563 4.2 24.9 1.0
ND1 B:HIS563 4.2 25.9 1.0
ND1 B:HIS529 4.2 25.6 1.0
CG B:HIS529 4.2 27.8 1.0
CB B:ASP564 4.3 26.2 1.0
CB B:ASP674 4.4 29.4 1.0
NE2 B:HIS525 4.4 33.8 1.0
O B:HOH953 4.6 28.1 1.0
CG2 B:VAL533 4.8 27.0 1.0
O B:ASP674 4.8 27.5 1.0
CA B:ASP674 4.8 27.6 1.0

Zinc binding site 3 out of 4 in 5sig

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea


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]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.5
occ:1.00
 OD2 C:ASP564 2.1 26.4 1.0
O C:HOH931 2.1 26.0 1.0
OD1 C:ASP674 2.1 28.4 1.0
NE2 C:HIS563 2.1 29.2 1.0
NE2 C:HIS529 2.2 28.5 1.0
O C:HOH995 2.3 38.1 1.0
CD2 C:HIS563 3.0 27.2 1.0
CG C:ASP674 3.0 31.5 1.0
CG C:ASP564 3.1 26.4 1.0
CD2 C:HIS529 3.1 30.2 1.0
CE1 C:HIS529 3.2 31.0 1.0
CE1 C:HIS563 3.2 27.6 1.0
OD2 C:ASP674 3.3 33.2 1.0
OD1 C:ASP564 3.6 26.2 1.0
MG C:MG802 3.9 31.3 1.0
CD2 C:HIS525 4.1 34.1 1.0
O C:HOH1011 4.1 29.9 1.0
O C:HOH1016 4.1 45.0 1.0
CG C:HIS563 4.2 26.8 1.0
CB C:ASP564 4.2 26.5 1.0
ND1 C:HIS563 4.3 27.6 1.0
CG C:HIS529 4.3 30.8 1.0
ND1 C:HIS529 4.3 29.5 1.0
CB C:ASP674 4.4 30.9 1.0
NE2 C:HIS525 4.4 36.2 1.0
O C:HOH947 4.6 33.6 1.0
CG2 C:VAL533 4.7 28.9 1.0
CA C:ASP674 4.8 31.1 1.0
O C:ASP674 4.9 31.3 1.0

Zinc binding site 4 out of 4 in 5sig

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[(4- Methoxyphenyl)Methyl]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea


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]-1-[(4-Oxo-3H-Quinazolin-2-Yl)Methyl]-3- Phenylurea within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:41.7
occ:1.00
 O D:HOH909 2.1 31.1 1.0
NE2 D:HIS563 2.1 33.4 1.0
NE2 D:HIS529 2.2 37.9 1.0
OD2 D:ASP564 2.2 39.5 1.0
OD1 D:ASP674 2.2 35.4 1.0
O D:HOH955 2.4 39.2 1.0
CD2 D:HIS563 3.0 35.5 1.0
CG D:ASP564 3.1 36.3 1.0
CG D:ASP674 3.1 37.6 1.0
CD2 D:HIS529 3.1 40.3 1.0
CE1 D:HIS563 3.2 35.6 1.0
CE1 D:HIS529 3.2 41.1 1.0
OD2 D:ASP674 3.3 39.9 1.0
OD1 D:ASP564 3.5 36.5 1.0
O D:HOH956 3.9 52.0 1.0
MG D:MG802 3.9 39.0 1.0
O D:HOH970 4.1 34.8 1.0
CG D:HIS563 4.2 34.3 1.0
CB D:ASP564 4.2 35.9 1.0
CD2 D:HIS525 4.2 41.2 1.0
ND1 D:HIS563 4.2 34.7 1.0
ND1 D:HIS529 4.3 39.3 1.0
CG D:HIS529 4.3 36.7 1.0
CB D:ASP674 4.5 38.7 1.0
NE2 D:HIS525 4.6 44.2 1.0
O D:HOH918 4.6 39.7 1.0
CG2 D:VAL533 4.7 39.6 1.0
O D:ASP674 4.8 34.9 1.0
CA D:ASP674 4.9 36.8 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 05:45:11 2024

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