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Zinc in PDB 5sjf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One, PDB code: 5sjf was solved by C.Joseph, J.Benz, A.Flohr, R.M.Rodriguez-Sarmiento, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.95 / 2.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.77, 136.77, 236.65, 90, 90, 120
R / Rfree (%) 18.8 / 22.7

Other elements in 5sjf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One also contains other interesting chemical elements:

Fluorine (F) 12 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One (pdb code 5sjf). 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 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One, PDB code: 5sjf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjf

Go back to Zinc Binding Sites List in 5sjf
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-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 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:36.7
occ:1.00
 OD2 A:ASP564 2.1 34.2 1.0
NE2 A:HIS563 2.1 29.9 1.0
NE2 A:HIS529 2.2 32.5 1.0
OD1 A:ASP674 2.2 36.1 1.0
O A:HOH980 2.2 34.4 1.0
O A:HOH952 2.3 32.2 1.0
CD2 A:HIS563 3.0 32.2 1.0
CG A:ASP674 3.1 32.5 1.0
CE1 A:HIS529 3.1 33.6 1.0
CG A:ASP564 3.1 33.5 1.0
CE1 A:HIS563 3.2 31.2 1.0
CD2 A:HIS529 3.2 33.0 1.0
OD2 A:ASP674 3.4 35.7 1.0
OD1 A:ASP564 3.7 31.9 1.0
MG A:MG802 3.9 29.8 1.0
O A:HOH1001 4.2 34.8 1.0
CG A:HIS563 4.2 29.5 1.0
O A:HOH960 4.2 31.8 1.0
ND1 A:HIS563 4.2 30.7 1.0
CD2 A:HIS525 4.2 31.8 1.0
ND1 A:HIS529 4.2 32.0 1.0
CB A:ASP564 4.3 33.5 1.0
CG A:HIS529 4.3 32.1 1.0
CB A:ASP674 4.5 33.7 1.0
NE2 A:HIS525 4.5 35.6 1.0
O A:HOH929 4.8 34.1 1.0
CG2 A:VAL533 4.8 29.7 1.0
CA A:ASP674 4.9 31.5 1.0
O A:ASP674 4.9 33.4 1.0

Zinc binding site 2 out of 4 in 5sjf

Go back to Zinc Binding Sites List in 5sjf
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-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 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:35.0
occ:1.00
 OD2 B:ASP564 2.2 32.7 1.0
NE2 B:HIS529 2.2 29.7 1.0
NE2 B:HIS563 2.2 27.7 1.0
OD1 B:ASP674 2.2 32.6 1.0
O B:HOH995 2.3 33.0 1.0
O B:HOH962 2.3 29.3 1.0
CG B:ASP674 3.1 30.5 1.0
CD2 B:HIS563 3.1 28.9 1.0
CE1 B:HIS529 3.2 29.8 1.0
CD2 B:HIS529 3.2 30.6 1.0
CE1 B:HIS563 3.2 28.2 1.0
CG B:ASP564 3.2 29.8 1.0
OD2 B:ASP674 3.3 32.3 1.0
OD1 B:ASP564 3.7 30.9 1.0
MG B:MG802 3.9 28.7 1.0
O B:HOH1008 4.0 31.3 1.0
O B:HOH963 4.1 28.6 1.0
CD2 B:HIS525 4.1 32.6 1.0
ND1 B:HIS529 4.3 29.6 1.0
ND1 B:HIS563 4.3 29.6 1.0
CG B:HIS563 4.3 28.5 1.0
CG B:HIS529 4.3 29.2 1.0
CB B:ASP564 4.4 30.7 1.0
NE2 B:HIS525 4.4 33.0 1.0
CB B:ASP674 4.5 30.1 1.0
O B:HOH959 4.7 31.0 1.0
CG2 B:VAL533 4.8 29.5 1.0
O B:ASP674 4.9 29.4 1.0
CA B:ASP674 4.9 29.1 1.0

Zinc binding site 3 out of 4 in 5sjf

Go back to Zinc Binding Sites List in 5sjf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-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 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.4
occ:1.00
 NE2 C:HIS529 2.1 31.4 1.0
O C:HOH988 2.2 34.5 1.0
OD2 C:ASP564 2.2 28.6 1.0
NE2 C:HIS563 2.2 29.0 1.0
OD1 C:ASP674 2.2 29.4 1.0
O C:HOH914 2.2 29.6 1.0
CG C:ASP674 3.0 31.1 1.0
CD2 C:HIS563 3.0 27.6 1.0
CE1 C:HIS529 3.1 35.5 1.0
CD2 C:HIS529 3.1 31.0 1.0
CG C:ASP564 3.2 30.8 1.0
OD2 C:ASP674 3.2 33.7 1.0
CE1 C:HIS563 3.2 27.4 1.0
OD1 C:ASP564 3.7 31.1 1.0
MG C:MG802 3.9 30.4 1.0
CD2 C:HIS525 4.1 34.3 1.0
O C:HOH960 4.2 39.3 1.0
ND1 C:HIS529 4.2 31.4 1.0
CG C:HIS563 4.2 27.4 1.0
CG C:HIS529 4.3 30.5 1.0
ND1 C:HIS563 4.3 27.8 1.0
O C:HOH1024 4.3 32.9 1.0
CB C:ASP564 4.3 31.2 1.0
NE2 C:HIS525 4.4 34.6 1.0
CB C:ASP674 4.4 30.7 1.0
O C:HOH940 4.6 31.1 1.0
CG2 C:VAL533 4.7 31.7 1.0
CA C:ASP674 4.8 30.5 1.0
O C:ASP674 4.9 30.0 1.0

Zinc binding site 4 out of 4 in 5sjf

Go back to Zinc Binding Sites List in 5sjf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-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 3-(2- Quinolin-4-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin-4- One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:45.5
occ:1.00
 NE2 D:HIS529 2.1 45.0 1.0
OD2 D:ASP564 2.2 41.2 1.0
O D:HOH950 2.2 36.9 1.0
NE2 D:HIS563 2.2 35.4 1.0
OD1 D:ASP674 2.3 41.2 1.0
O D:HOH966 2.4 45.4 1.0
CE1 D:HIS529 3.0 42.3 1.0
CD2 D:HIS563 3.1 36.6 1.0
CD2 D:HIS529 3.1 44.6 1.0
CG D:ASP564 3.2 36.5 1.0
CG D:ASP674 3.2 39.6 1.0
CE1 D:HIS563 3.3 35.9 1.0
OD2 D:ASP674 3.4 37.0 1.0
OD1 D:ASP564 3.7 39.5 1.0
MG D:MG802 4.0 41.2 1.0
ND1 D:HIS529 4.2 42.4 1.0
O D:HOH961 4.2 38.4 1.0
O D:HOH916 4.2 45.8 1.0
CG D:HIS529 4.2 41.3 1.0
CD2 D:HIS525 4.2 44.5 1.0
CG D:HIS563 4.3 37.3 1.0
CB D:ASP564 4.3 37.1 1.0
ND1 D:HIS563 4.4 36.3 1.0
CB D:ASP674 4.5 39.3 1.0
NE2 D:HIS525 4.6 48.0 1.0
O D:HOH918 4.7 40.6 1.0
CG2 D:VAL533 4.7 37.8 1.0
O D:ASP674 4.8 43.1 1.0
CA D:ASP674 4.9 38.7 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 05:58:45 2024

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