Atomistry » Zinc » PDB 5sk6-5sl9 » 5skh
Atomistry »
  Zinc »
    PDB 5sk6-5sl9 »
      5skh »

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

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Fluorophenyl)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- (3-Fluorophenyl)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- (3-Fluorophenyl)Pyrazol-3-Yl]-1-[3-(Trifluoromethoxy) Phenyl]Pyridazin-4-One, PDB code: 5skh 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) 41.38 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.11, 135.11, 234.43, 90, 90, 120
R / Rfree (%) 19.4 / 23.7

Other elements in 5skh:

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

Fluorine (F) 16 atoms
Magnesium (Mg) 4 atoms
Chlorine (Cl) 1 atom
Praseodymium (Pr) 8 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5skh

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

b:28.6
occ:1.00
 OD2 A:ASP564 2.0 25.2 1.0
NE2 A:HIS529 2.1 28.7 1.0
OD1 A:ASP674 2.2 29.0 1.0
NE2 A:HIS563 2.2 23.9 1.0
O A:HOH994 2.2 26.7 1.0
O A:HOH940 2.4 21.9 1.0
CG A:ASP564 3.1 24.9 1.0
CG A:ASP674 3.1 27.6 1.0
CD2 A:HIS529 3.1 28.6 1.0
CE1 A:HIS529 3.1 27.9 1.0
CD2 A:HIS563 3.1 22.8 1.0
CE1 A:HIS563 3.2 24.3 1.0
OD2 A:ASP674 3.3 29.6 1.0
OD1 A:ASP564 3.6 23.9 1.0
MG A:MG802 3.9 20.7 1.0
O A:HOH1006 4.0 21.9 1.0
CD2 A:HIS525 4.1 28.0 1.0
ND1 A:HIS529 4.2 26.3 1.0
CG A:HIS529 4.2 26.3 1.0
O A:HOH979 4.2 28.1 1.0
CG A:HIS563 4.3 24.5 1.0
CB A:ASP564 4.3 23.8 1.0
ND1 A:HIS563 4.3 23.6 1.0
NE2 A:HIS525 4.4 27.7 1.0
CB A:ASP674 4.4 27.9 1.0
O A:HOH929 4.6 23.7 1.0
CG2 A:VAL533 4.7 20.4 1.0
O A:ASP674 4.8 28.1 1.0
CA A:ASP674 4.9 26.2 1.0

Zinc binding site 2 out of 4 in 5skh

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

b:28.3
occ:1.00
 OD2 B:ASP564 2.1 22.6 1.0
NE2 B:HIS563 2.1 21.2 1.0
NE2 B:HIS529 2.1 21.1 1.0
O B:HOH950 2.2 18.7 1.0
OD1 B:ASP674 2.2 25.1 1.0
O B:HOH1002 2.3 26.6 1.0
CD2 B:HIS563 3.0 20.1 1.0
CG B:ASP674 3.1 24.9 1.0
CG B:ASP564 3.1 23.2 1.0
CE1 B:HIS563 3.1 21.6 1.0
CD2 B:HIS529 3.1 23.3 1.0
CE1 B:HIS529 3.2 23.8 1.0
OD2 B:ASP674 3.3 24.6 1.0
OD1 B:ASP564 3.6 23.0 1.0
MG B:MG802 3.9 18.2 1.0
O B:HOH969 4.0 22.7 1.0
CD2 B:HIS525 4.2 23.2 1.0
O B:HOH981 4.2 24.9 1.0
CG B:HIS563 4.2 22.2 1.0
ND1 B:HIS563 4.2 21.1 1.0
ND1 B:HIS529 4.3 22.4 1.0
CB B:ASP564 4.3 23.3 1.0
CG B:HIS529 4.3 22.4 1.0
NE2 B:HIS525 4.4 23.8 1.0
CB B:ASP674 4.4 25.4 1.0
O B:HOH948 4.6 23.3 1.0
CG2 B:VAL533 4.7 21.8 1.0
CA B:ASP674 4.8 25.3 1.0
O B:ASP674 4.8 23.7 1.0

Zinc binding site 3 out of 4 in 5skh

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

b:29.8
occ:1.00
 NE2 C:HIS529 2.1 24.1 1.0
O C:HOH922 2.1 24.4 1.0
OD1 C:ASP674 2.1 21.9 1.0
OD2 C:ASP564 2.1 24.4 1.0
NE2 C:HIS563 2.2 25.8 1.0
O C:HOH1008 2.2 29.5 1.0
CE1 C:HIS529 3.0 25.8 1.0
CG C:ASP674 3.0 25.6 1.0
CD2 C:HIS563 3.1 23.9 1.0
CD2 C:HIS529 3.1 24.8 1.0
CG C:ASP564 3.1 22.8 1.0
OD2 C:ASP674 3.2 26.7 1.0
CE1 C:HIS563 3.3 24.6 1.0
OD1 C:ASP564 3.6 22.1 1.0
MG C:MG802 3.9 20.8 1.0
O C:HOH1018 4.0 22.2 1.0
ND1 C:HIS529 4.1 24.7 1.0
CD2 C:HIS525 4.2 29.3 1.0
CG C:HIS529 4.2 24.1 1.0
O C:HOH965 4.2 30.0 1.0
CG C:HIS563 4.3 23.0 1.0
ND1 C:HIS563 4.3 23.1 1.0
CB C:ASP674 4.3 26.4 1.0
CB C:ASP564 4.3 21.7 1.0
NE2 C:HIS525 4.4 29.1 1.0
O C:HOH931 4.6 28.7 1.0
CA C:ASP674 4.7 26.1 1.0
CG2 C:VAL533 4.7 24.2 1.0
O C:ASP674 4.8 27.3 1.0

Zinc binding site 4 out of 4 in 5skh

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

b:35.4
occ:1.00
 OD2 D:ASP564 2.1 33.1 1.0
NE2 D:HIS529 2.1 33.3 1.0
NE2 D:HIS563 2.2 25.7 1.0
OD1 D:ASP674 2.2 34.9 1.0
O D:HOH939 2.2 23.6 1.0
O D:HOH982 2.2 26.7 1.0
CD2 D:HIS563 3.0 27.2 1.0
CG D:ASP674 3.1 33.1 1.0
CD2 D:HIS529 3.1 33.4 1.0
CG D:ASP564 3.1 29.9 1.0
CE1 D:HIS529 3.2 35.3 1.0
CE1 D:HIS563 3.3 28.7 1.0
OD2 D:ASP674 3.3 33.7 1.0
OD1 D:ASP564 3.7 28.4 1.0
MG D:MG802 3.9 30.6 1.0
O D:HOH943 4.1 28.6 1.0
CD2 D:HIS525 4.2 36.2 1.0
CG D:HIS563 4.2 26.9 1.0
O D:HOH976 4.2 31.9 1.0
CB D:ASP564 4.2 30.6 1.0
ND1 D:HIS529 4.2 32.8 1.0
CG D:HIS529 4.2 31.3 1.0
ND1 D:HIS563 4.3 26.8 1.0
CB D:ASP674 4.4 32.4 1.0
NE2 D:HIS525 4.5 39.1 1.0
O D:HOH949 4.5 33.3 1.0
CG2 D:VAL533 4.7 31.9 1.0
O D:ASP674 4.7 32.7 1.0
CA D:ASP674 4.9 31.8 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: Fri Apr 7 23:09:17 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy