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Zinc in PDB 5shz: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One, PDB code: 5shz was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.53 / 2.55
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.456, 135.456, 234.872, 90, 90, 120
R / Rfree (%) 18.1 / 24.3

Other elements in 5shz:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-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 3-[2- (3-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One (pdb code 5shz). 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-Ethynylphenyl)Pyrazol-3-Yl]-1-Phenylpyridazin-4-One, PDB code: 5shz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shz

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

b:45.3
occ:1.00
 OD2 A:ASP564 1.9 49.3 1.0
OD1 A:ASP674 2.0 53.7 1.0
NE2 A:HIS563 2.0 38.8 1.0
NE2 A:HIS529 2.2 36.0 1.0
O A:HOH917 2.4 38.8 1.0
O A:HOH904 2.5 32.3 1.0
CG A:ASP674 2.9 42.9 1.0
CD2 A:HIS563 2.9 39.3 1.0
CG A:ASP564 3.0 40.9 1.0
CD2 A:HIS529 3.1 38.2 1.0
CE1 A:HIS563 3.1 39.9 1.0
OD2 A:ASP674 3.2 51.3 1.0
CE1 A:HIS529 3.2 38.1 1.0
OD1 A:ASP564 3.6 37.1 1.0
MG A:MG802 3.8 25.3 1.0
CD2 A:HIS525 4.0 47.9 1.0
O A:HOH918 4.1 41.9 1.0
CG A:HIS563 4.1 37.3 1.0
ND1 A:HIS563 4.2 33.3 1.0
CB A:ASP564 4.2 34.6 1.0
CG A:HIS529 4.3 38.1 1.0
NE2 A:HIS525 4.3 45.5 1.0
ND1 A:HIS529 4.3 38.4 1.0
CB A:ASP674 4.3 46.9 1.0
O A:HOH902 4.4 27.0 1.0
O A:HOH911 4.5 46.7 1.0
CA A:ASP674 4.8 42.9 1.0
CG2 A:VAL533 4.8 34.0 1.0
O A:ASP674 4.9 49.7 1.0

Zinc binding site 2 out of 4 in 5shz

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

b:41.1
occ:1.00
 OD2 B:ASP564 2.0 40.7 1.0
NE2 B:HIS563 2.1 34.4 1.0
NE2 B:HIS529 2.1 27.2 1.0
OD1 B:ASP674 2.1 39.6 1.0
O B:HOH910 2.3 19.4 1.0
O B:HOH917 2.6 33.2 1.0
CG B:ASP674 2.9 35.0 1.0
CD2 B:HIS563 3.0 30.6 1.0
OD2 B:ASP674 3.1 41.0 1.0
CG B:ASP564 3.1 36.1 1.0
CD2 B:HIS529 3.1 32.3 1.0
CE1 B:HIS529 3.1 28.6 1.0
CE1 B:HIS563 3.2 37.0 1.0
OD1 B:ASP564 3.7 33.2 1.0
MG B:MG802 3.9 23.4 1.0
O B:HOH924 4.0 25.8 1.0
CB B:ASP564 4.2 32.5 1.0
CG B:HIS563 4.2 30.7 1.0
CD2 B:HIS525 4.2 52.4 1.0
ND1 B:HIS529 4.2 28.8 1.0
CG B:HIS529 4.2 30.4 1.0
ND1 B:HIS563 4.2 34.4 1.0
CB B:ASP674 4.3 37.5 1.0
NE2 B:HIS525 4.5 44.8 1.0
O B:HOH905 4.6 32.0 1.0
CA B:ASP674 4.7 35.2 1.0
CG2 B:VAL533 4.7 33.0 1.0
O B:ASP674 4.9 41.5 1.0

Zinc binding site 3 out of 4 in 5shz

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

b:43.0
occ:1.00
 OD2 C:ASP564 2.0 45.0 1.0
NE2 C:HIS529 2.0 32.5 1.0
OD1 C:ASP674 2.1 48.3 1.0
NE2 C:HIS563 2.2 35.2 1.0
O C:HOH903 2.3 29.4 1.0
CG C:ASP674 2.8 40.6 1.0
OD2 C:ASP674 2.8 45.5 1.0
CD2 C:HIS529 3.0 35.4 1.0
CE1 C:HIS529 3.0 33.6 1.0
CG C:ASP564 3.1 40.3 1.0
CD2 C:HIS563 3.2 34.5 1.0
CE1 C:HIS563 3.2 37.4 1.0
OD1 C:ASP564 3.7 40.8 1.0
MG C:MG802 3.8 32.2 1.0
CD2 C:HIS525 4.0 47.3 1.0
CG C:HIS529 4.1 34.5 1.0
ND1 C:HIS529 4.1 34.4 1.0
NE2 C:HIS525 4.2 53.4 1.0
CB C:ASP674 4.3 40.5 1.0
ND1 C:HIS563 4.3 34.5 1.0
CG C:HIS563 4.3 36.4 1.0
CB C:ASP564 4.3 35.8 1.0
O C:HOH902 4.6 37.5 1.0
O C:HOH912 4.6 43.2 1.0
CA C:ASP674 4.7 41.7 1.0
CG2 C:VAL533 4.8 32.1 1.0
O C:ASP674 4.8 43.5 1.0

Zinc binding site 4 out of 4 in 5shz

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

b:55.1
occ:1.00
 O D:HOH904 2.1 37.6 1.0
NE2 D:HIS563 2.1 45.1 1.0
OD1 D:ASP674 2.1 61.1 1.0
OD2 D:ASP564 2.2 61.4 1.0
NE2 D:HIS529 2.2 47.9 1.0
O D:HOH912 2.5 43.3 1.0
CD2 D:HIS563 3.0 44.8 1.0
CG D:ASP674 3.1 53.6 1.0
CE1 D:HIS563 3.2 45.2 1.0
CE1 D:HIS529 3.2 47.2 1.0
CD2 D:HIS529 3.2 48.7 1.0
CG D:ASP564 3.2 53.6 1.0
OD2 D:ASP674 3.4 57.8 1.0
MG D:MG802 3.9 43.5 1.0
OD1 D:ASP564 3.9 51.1 1.0
CG D:HIS563 4.2 50.4 1.0
CD2 D:HIS525 4.2 54.2 1.0
ND1 D:HIS563 4.2 41.8 1.0
CB D:ASP564 4.3 52.8 1.0
ND1 D:HIS529 4.3 54.8 1.0
O D:HOH911 4.4 48.7 1.0
CG D:HIS529 4.4 45.0 1.0
CB D:ASP674 4.4 58.2 1.0
NE2 D:HIS525 4.5 47.6 1.0
O D:HOH903 4.6 51.5 1.0
CG2 D:VAL533 4.6 46.5 1.0
O D:ASP674 4.6 72.9 1.0
CA D:ASP674 4.8 60.2 1.0
O D:HOH907 4.8 38.6 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: Fri Apr 7 22:35:22 2023

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