Zinc in PDB 5skd: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-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- (2,5-Difluorophenyl)Pyrazol-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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skd 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) 43.61 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.64, 135.64, 234.83, 90, 90, 120
R / Rfree (%) 16.3 / 17.8

Other elements in 5skd:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One also contains other interesting chemical elements:

Praseodymium (Pr) 8 atoms
Fluorine (F) 25 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5skd

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-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- (2,5-Difluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.8
occ:1.00
 OD2 A:ASP564 2.0 33.6 1.0
NE2 A:HIS529 2.1 31.5 1.0
NE2 A:HIS563 2.2 27.5 1.0
OD1 A:ASP674 2.2 27.4 1.0
O A:HOH950 2.3 27.9 1.0
O A:HOH978 2.4 35.4 1.0
CG A:ASP564 3.0 31.7 1.0
CD2 A:HIS563 3.1 28.1 1.0
CE1 A:HIS529 3.1 35.1 1.0
CE1 A:HIS563 3.1 30.1 1.0
CD2 A:HIS529 3.1 30.6 1.0
CG A:ASP674 3.2 31.8 1.0
OD2 A:ASP674 3.5 28.6 1.0
OD1 A:ASP564 3.5 30.6 1.0
MG A:MG802 3.9 26.1 1.0
O A:HOH995 3.9 22.2 1.0
CD2 A:HIS525 4.2 30.7 1.0
CG A:HIS563 4.2 29.9 1.0
ND1 A:HIS563 4.2 30.0 1.0
CB A:ASP564 4.2 30.1 1.0
O A:HOH929 4.2 31.0 1.0
ND1 A:HIS529 4.2 33.2 1.0
CG A:HIS529 4.3 30.6 1.0
O A:HOH923 4.4 25.5 1.0
NE2 A:HIS525 4.5 31.0 1.0
CB A:ASP674 4.5 29.1 1.0
CG2 A:VAL533 4.7 26.6 1.0
O A:ASP674 4.8 29.3 1.0
CA A:ASP674 4.9 29.0 1.0

Zinc binding site 2 out of 4 in 5skd

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

b:30.9
occ:1.00
 NE2 B:HIS563 2.0 28.0 1.0
OD2 B:ASP564 2.1 29.6 1.0
OD1 B:ASP674 2.1 34.8 1.0
O B:HOH951 2.2 23.2 1.0
NE2 B:HIS529 2.3 24.7 1.0
O B:HOH971 2.3 35.9 1.0
CD2 B:HIS563 3.0 25.5 1.0
CG B:ASP674 3.0 31.6 1.0
CG B:ASP564 3.0 28.5 1.0
CE1 B:HIS563 3.1 30.2 1.0
CD2 B:HIS529 3.2 25.1 1.0
OD2 B:ASP674 3.2 30.6 1.0
CE1 B:HIS529 3.3 27.2 1.0
OD1 B:ASP564 3.5 27.8 1.0
MG B:MG802 3.9 27.8 1.0
O B:HOH980 4.0 21.4 1.0
O B:HOH962 4.1 32.9 1.0
CG B:HIS563 4.1 26.9 1.0
ND1 B:HIS563 4.2 27.8 1.0
CD2 B:HIS525 4.2 24.4 1.0
CB B:ASP564 4.2 27.5 1.0
CG B:HIS529 4.4 25.4 1.0
ND1 B:HIS529 4.4 24.1 1.0
CB B:ASP674 4.4 29.5 1.0
NE2 B:HIS525 4.5 28.1 1.0
O B:HOH952 4.6 31.7 1.0
O B:ASP674 4.8 30.1 1.0
CG2 B:VAL533 4.8 26.9 1.0
CA B:ASP674 4.9 29.2 1.0

Zinc binding site 3 out of 4 in 5skd

Go back to Zinc Binding Sites List in 5skd
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (2,5-Difluorophenyl)Pyrazol-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- (2,5-Difluorophenyl)Pyrazol-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 23.0 1.0
OD2 C:ASP564 2.1 28.2 1.0
O C:HOH983 2.2 36.9 1.0
O C:HOH942 2.2 25.9 1.0
NE2 C:HIS563 2.2 30.3 1.0
OD1 C:ASP674 2.2 29.5 1.0
CE1 C:HIS529 3.0 26.9 1.0
CD2 C:HIS563 3.1 28.2 1.0
CG C:ASP564 3.1 29.9 1.0
CD2 C:HIS529 3.1 27.5 1.0
CG C:ASP674 3.2 30.9 1.0
CE1 C:HIS563 3.3 29.8 1.0
OD2 C:ASP674 3.5 29.1 1.0
OD1 C:ASP564 3.6 30.3 1.0
MG C:MG802 4.0 24.1 1.0
ND1 C:HIS529 4.1 26.2 1.0
CG C:HIS529 4.2 27.6 1.0
CG C:HIS563 4.2 29.5 1.0
CD2 C:HIS525 4.3 34.2 1.0
O C:HOH1009 4.3 24.9 1.0
ND1 C:HIS563 4.3 28.2 1.0
CB C:ASP564 4.4 27.4 1.0
O C:HOH926 4.5 33.3 1.0
CB C:ASP674 4.5 30.9 1.0
NE2 C:HIS525 4.5 34.8 1.0
O C:HOH955 4.6 27.7 1.0
CG2 C:VAL533 4.8 25.4 1.0
O C:ASP674 4.8 32.4 1.0
CA C:ASP674 4.8 31.8 1.0

Zinc binding site 4 out of 4 in 5skd

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

b:39.3
occ:1.00
 O D:HOH909 1.9 39.2 1.0
NE2 D:HIS529 2.1 34.1 1.0
OD1 D:ASP674 2.2 35.0 1.0
NE2 D:HIS563 2.2 28.9 1.0
OD2 D:ASP564 2.2 35.8 1.0
O D:HOH958 2.2 41.9 1.0
CG D:ASP674 3.0 32.0 1.0
CD2 D:HIS563 3.0 30.8 1.0
CD2 D:HIS529 3.1 36.1 1.0
CE1 D:HIS529 3.2 34.5 1.0
OD2 D:ASP674 3.2 33.9 1.0
CG D:ASP564 3.2 33.6 1.0
CE1 D:HIS563 3.2 29.6 1.0
OD1 D:ASP564 3.7 31.0 1.0
MG D:MG802 3.9 32.2 1.0
O D:HOH922 4.2 39.7 1.0
CG D:HIS563 4.2 29.7 1.0
CD2 D:HIS525 4.2 39.8 1.0
CG D:HIS529 4.2 33.1 1.0
O D:HOH978 4.2 29.8 1.0
ND1 D:HIS529 4.3 32.6 1.0
ND1 D:HIS563 4.3 30.3 1.0
CB D:ASP564 4.3 33.3 1.0
CB D:ASP674 4.4 34.3 1.0
NE2 D:HIS525 4.5 41.1 1.0
O D:HOH935 4.6 34.8 1.0
CG2 D:VAL533 4.7 34.6 1.0
O D:ASP674 4.7 35.9 1.0
CA D:ASP674 4.8 32.9 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 07:35:36 2024

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