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Zinc in PDB 5si4: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-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- Naphthalen-1-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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One, PDB code: 5si4 was solved by C.Joseph, J.Benz, A.Flohr, M.Rogers-Evans, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.39
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.86, 135.86, 235.62, 90, 90, 120
R / Rfree (%) 17.5 / 23.8

Other elements in 5si4:

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

Magnesium (Mg) 4 atoms
Fluorine (F) 21 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One (pdb code 5si4). 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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One, PDB code: 5si4:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si4

Go back to Zinc Binding Sites List in 5si4
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.9
occ:1.00
 NE2 A:HIS563 2.0 28.2 1.0
OD2 A:ASP564 2.1 37.8 1.0
OD1 A:ASP674 2.1 51.1 1.0
NE2 A:HIS529 2.1 34.0 1.0
O A:HOH908 2.2 30.5 1.0
O A:HOH954 2.3 35.6 1.0
CG A:ASP674 2.9 40.3 1.0
CD2 A:HIS563 3.0 29.9 1.0
CE1 A:HIS563 3.0 33.4 1.0
CE1 A:HIS529 3.1 34.5 1.0
CD2 A:HIS529 3.1 33.7 1.0
CG A:ASP564 3.1 34.8 1.0
OD2 A:ASP674 3.1 44.7 1.0
OD1 A:ASP564 3.7 35.7 1.0
MG A:MG802 3.9 35.5 1.0
ND1 A:HIS563 4.1 28.6 1.0
CG A:HIS563 4.1 30.8 1.0
CD2 A:HIS525 4.1 31.7 1.0
O A:HOH957 4.2 40.8 1.0
ND1 A:HIS529 4.2 34.7 1.0
CB A:ASP564 4.2 31.6 1.0
CG A:HIS529 4.2 31.9 1.0
O A:HOH922 4.3 30.8 1.0
CB A:ASP674 4.3 37.3 1.0
NE2 A:HIS525 4.3 32.6 1.0
O A:HOH914 4.7 25.8 1.0
CG2 A:VAL533 4.7 29.2 1.0
CA A:ASP674 4.8 33.8 1.0
O A:ASP674 4.9 34.5 1.0

Zinc binding site 2 out of 4 in 5si4

Go back to Zinc Binding Sites List in 5si4
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.1
occ:1.00
 NE2 B:HIS529 2.1 28.5 1.0
NE2 B:HIS563 2.2 27.5 1.0
OD2 B:ASP564 2.2 30.6 1.0
O B:HOH944 2.2 28.5 1.0
OD1 B:ASP674 2.2 34.2 1.0
O B:HOH974 2.5 31.5 1.0
CE1 B:HIS529 3.0 30.1 1.0
CD2 B:HIS563 3.0 29.4 1.0
CG B:ASP674 3.1 32.3 1.0
CG B:ASP564 3.1 30.6 1.0
CD2 B:HIS529 3.2 29.5 1.0
CE1 B:HIS563 3.2 28.3 1.0
OD2 B:ASP674 3.4 33.0 1.0
OD1 B:ASP564 3.6 30.3 1.0
O B:HOH978 3.9 22.9 1.0
MG B:MG802 4.0 28.8 1.0
CD2 B:HIS525 4.2 32.6 1.0
ND1 B:HIS529 4.2 31.3 1.0
CG B:HIS563 4.2 30.2 1.0
ND1 B:HIS563 4.3 29.6 1.0
CG B:HIS529 4.3 30.3 1.0
CB B:ASP564 4.3 30.1 1.0
O B:HOH933 4.3 32.2 1.0
CB B:ASP674 4.5 34.6 1.0
NE2 B:HIS525 4.5 31.9 1.0
CG2 B:VAL533 4.8 30.2 1.0
O B:ASP674 4.8 31.9 1.0
CA B:ASP674 4.8 31.6 1.0
O B:HOH932 4.9 27.0 1.0

Zinc binding site 3 out of 4 in 5si4

Go back to Zinc Binding Sites List in 5si4
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:38.2
occ:1.00
 NE2 C:HIS529 2.1 29.7 1.0
O C:HOH973 2.1 41.9 1.0
OD2 C:ASP564 2.1 31.1 1.0
O C:HOH938 2.1 23.2 1.0
OD1 C:ASP674 2.2 33.5 1.0
NE2 C:HIS563 2.2 25.7 1.0
CD2 C:HIS529 3.0 31.9 1.0
CG C:ASP674 3.1 30.2 1.0
CE1 C:HIS529 3.1 31.9 1.0
CD2 C:HIS563 3.2 24.6 1.0
CE1 C:HIS563 3.2 26.4 1.0
CG C:ASP564 3.2 30.3 1.0
OD2 C:ASP674 3.3 33.1 1.0
OD1 C:ASP564 3.8 30.2 1.0
MG C:MG802 3.9 29.8 1.0
CD2 C:HIS525 4.1 35.3 1.0
CG C:HIS529 4.2 31.0 1.0
NE2 C:HIS525 4.2 36.9 1.0
ND1 C:HIS529 4.2 33.6 1.0
ND1 C:HIS563 4.3 25.8 1.0
O C:HOH922 4.3 27.9 1.0
CG C:HIS563 4.3 25.2 1.0
CB C:ASP564 4.3 30.0 1.0
CB C:ASP674 4.4 32.5 1.0
O C:HOH1017 4.5 42.1 1.0
O C:HOH950 4.6 29.2 1.0
CG2 C:VAL533 4.7 31.4 1.0
CA C:ASP674 4.8 30.8 1.0
O C:ASP674 4.9 33.4 1.0

Zinc binding site 4 out of 4 in 5si4

Go back to Zinc Binding Sites List in 5si4
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Naphthalen-1-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- Naphthalen-1-Ylpyrazol-3-Yl)-1-[3-(Trifluoromethoxy)Phenyl]Pyridazin- 4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:55.6
occ:1.00
 OD1 D:ASP674 2.1 52.6 1.0
NE2 D:HIS563 2.1 37.0 1.0
OD2 D:ASP564 2.2 49.2 1.0
O D:HOH933 2.2 37.2 1.0
NE2 D:HIS529 2.2 50.6 1.0
O D:HOH919 2.3 33.7 1.0
CD2 D:HIS563 3.1 36.7 1.0
CG D:ASP674 3.1 50.3 1.0
CE1 D:HIS563 3.1 35.5 1.0
CE1 D:HIS529 3.2 49.5 1.0
CD2 D:HIS529 3.2 49.6 1.0
CG D:ASP564 3.2 47.7 1.0
OD2 D:ASP674 3.5 53.8 1.0
O D:HOH904 3.8 42.4 1.0
O D:HOH908 3.8 44.0 1.0
OD1 D:ASP564 3.9 45.4 1.0
MG D:MG802 4.1 50.2 1.0
CD2 D:HIS525 4.1 53.8 1.0
ND1 D:HIS563 4.2 35.3 1.0
CG D:HIS563 4.3 39.4 1.0
CB D:ASP564 4.3 48.8 1.0
ND1 D:HIS529 4.3 52.8 1.0
CG D:HIS529 4.3 47.7 1.0
NE2 D:HIS525 4.4 57.2 1.0
CB D:ASP674 4.5 50.9 1.0
CG2 D:VAL533 4.7 45.4 1.0
O D:ASP674 4.7 56.0 1.0
O D:HOH907 4.8 40.2 1.0
CA D:ASP674 4.8 51.6 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 05:41:13 2024

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