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Zinc in PDB 5sj4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One, PDB code: 5sj4 was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.48 / 2.77
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.14, 135.14, 235.843, 90, 90, 120
R / Rfree (%) 19.5 / 27.8

Other elements in 5sj4:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One 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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One (pdb code 5sj4). 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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One, PDB code: 5sj4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sj4

Go back to Zinc Binding Sites List in 5sj4
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:51.1
occ:1.00
 NE2 A:HIS563 2.0 47.7 1.0
OD2 A:ASP564 2.0 38.0 1.0
OD1 A:ASP674 2.1 47.7 1.0
NE2 A:HIS529 2.1 43.3 1.0
O A:HOH909 2.3 34.6 1.0
O A:HOH924 2.4 46.4 1.0
CE1 A:HIS563 2.8 47.3 1.0
CG A:ASP674 2.9 51.6 1.0
CD2 A:HIS529 2.9 47.6 1.0
OD2 A:ASP674 3.0 66.9 1.0
CD2 A:HIS563 3.0 48.2 1.0
CG A:ASP564 3.1 44.3 1.0
CE1 A:HIS529 3.3 45.8 1.0
OD1 A:ASP564 3.7 37.4 1.0
ND1 A:HIS563 3.9 52.7 1.0
CG A:HIS563 4.0 49.0 1.0
MG A:MG802 4.1 90.3 1.0
CG A:HIS529 4.1 39.6 1.0
O A:HOH926 4.2 53.5 1.0
CB A:ASP564 4.2 40.4 1.0
CB A:ASP674 4.3 47.4 1.0
ND1 A:HIS529 4.3 45.3 1.0
CD2 A:HIS525 4.4 51.5 1.0
NE2 A:HIS525 4.5 53.5 1.0
O A:HOH903 4.6 47.4 1.0
CG2 A:VAL533 4.7 48.4 1.0
CA A:ASP674 4.8 43.2 1.0

Zinc binding site 2 out of 4 in 5sj4

Go back to Zinc Binding Sites List in 5sj4
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:51.5
occ:1.00
 O B:HOH904 1.9 43.3 1.0
NE2 B:HIS563 1.9 46.8 1.0
OD2 B:ASP564 2.0 51.5 1.0
NE2 B:HIS529 2.1 38.8 1.0
OD1 B:ASP674 2.4 49.4 1.0
CD2 B:HIS563 2.9 47.4 1.0
CE1 B:HIS563 3.0 56.4 1.0
CD2 B:HIS529 3.0 44.1 1.0
CG B:ASP564 3.0 45.2 1.0
CG B:ASP674 3.1 48.6 1.0
OD2 B:ASP674 3.1 63.1 1.0
CE1 B:HIS529 3.1 37.8 1.0
OD1 B:ASP564 3.7 41.0 1.0
O B:HOH928 3.7 25.0 1.0
CG B:HIS563 4.0 45.0 1.0
MG B:MG802 4.0 58.5 1.0
ND1 B:HIS563 4.0 51.9 1.0
CD2 B:HIS525 4.1 54.7 1.0
CB B:ASP564 4.1 39.1 1.0
CG B:HIS529 4.2 41.3 1.0
ND1 B:HIS529 4.2 36.9 1.0
NE2 B:HIS525 4.3 50.5 1.0
CB B:ASP674 4.4 48.1 1.0
O B:HOH910 4.6 44.3 1.0
O B:HOH902 4.9 43.5 1.0
CA B:ASP674 4.9 46.1 1.0
CG2 B:VAL533 4.9 55.6 1.0
O B:ASP674 4.9 71.4 1.0

Zinc binding site 3 out of 4 in 5sj4

Go back to Zinc Binding Sites List in 5sj4
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:46.6
occ:1.00
 NE2 C:HIS563 1.9 38.1 1.0
OD2 C:ASP564 2.0 56.3 1.0
NE2 C:HIS529 2.1 50.5 1.0
O C:HOH914 2.2 17.2 1.0
O C:HOH917 2.3 52.5 1.0
OD1 C:ASP674 2.4 54.9 1.0
CD2 C:HIS563 2.8 43.1 1.0
CD2 C:HIS529 2.9 51.9 1.0
CE1 C:HIS563 3.0 39.6 1.0
CG C:ASP674 3.0 46.6 1.0
CG C:ASP564 3.1 49.3 1.0
OD2 C:ASP674 3.2 55.8 1.0
CE1 C:HIS529 3.2 52.1 1.0
OD1 C:ASP564 3.6 44.5 1.0
CG C:HIS563 4.0 40.6 1.0
ND1 C:HIS563 4.1 40.6 1.0
CG C:HIS529 4.1 50.3 1.0
O C:HOH937 4.2 47.8 1.0
MG C:MG802 4.2 44.7 1.0
O C:HOH934 4.2 35.1 1.0
CD2 C:HIS525 4.2 59.5 1.0
ND1 C:HIS529 4.2 50.1 1.0
CB C:ASP564 4.3 43.1 1.0
CB C:ASP674 4.3 45.5 1.0
O C:HOH918 4.4 36.8 1.0
CG2 C:VAL533 4.5 37.9 1.0
NE2 C:HIS525 4.7 64.4 1.0
CA C:ASP674 4.7 45.5 1.0
O C:ASP674 4.8 60.5 1.0

Zinc binding site 4 out of 4 in 5sj4

Go back to Zinc Binding Sites List in 5sj4
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One


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- Methyl-6-[2-(1-Methyl-4-Phenylimidazol-2-Yl)Ethyl]-5H-Pyrazolo[3,4- D]Pyrimidin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:60.9
occ:1.00
 NE2 D:HIS529 2.0 47.0 1.0
OD2 D:ASP564 2.0 75.1 1.0
NE2 D:HIS563 2.1 50.8 1.0
OD1 D:ASP674 2.1 60.8 1.0
O D:HOH912 2.1 23.8 1.0
O D:HOH915 2.6 45.7 1.0
CE1 D:HIS529 2.9 47.4 1.0
CD2 D:HIS529 3.0 54.1 1.0
CD2 D:HIS563 3.0 54.9 1.0
CG D:ASP564 3.1 62.2 1.0
CG D:ASP674 3.2 65.6 1.0
CE1 D:HIS563 3.2 57.5 1.0
OD2 D:ASP674 3.6 70.1 1.0
OD1 D:ASP564 3.6 60.7 1.0
O D:HOH904 3.7 40.0 1.0
ND1 D:HIS529 4.0 54.2 1.0
MG D:MG802 4.0 54.3 1.0
CG D:HIS529 4.1 54.2 1.0
CB D:ASP564 4.2 49.6 1.0
CG D:HIS563 4.2 59.2 1.0
CD2 D:HIS525 4.2 63.9 1.0
ND1 D:HIS563 4.3 55.9 1.0
NE2 D:HIS525 4.5 59.4 1.0
CB D:ASP674 4.5 71.5 1.0
O D:ASP674 4.7 80.3 1.0
CG2 D:VAL533 4.7 64.3 1.0
CA D:ASP674 4.9 65.6 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 05:56:26 2024

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