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Zinc in PDB 5sjx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline, PDB code: 5sjx was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.77 / 2.06
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.65, 135.65, 235.91, 90, 90, 120
R / Rfree (%) 18 / 23.7

Other elements in 5sjx:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline 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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline (pdb code 5sjx). 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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline, PDB code: 5sjx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjx

Go back to Zinc Binding Sites List in 5sjx
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.1
occ:1.00
 O A:HOH989 2.1 29.6 1.0
O A:HOH1017 2.1 33.7 1.0
NE2 A:HIS529 2.1 29.8 1.0
NE2 A:HIS563 2.2 23.1 1.0
OD2 A:ASP564 2.2 26.7 1.0
OD1 A:ASP674 2.2 32.7 1.0
CD2 A:HIS563 3.0 22.8 1.0
CD2 A:HIS529 3.0 27.0 1.0
CG A:ASP564 3.1 24.7 1.0
CG A:ASP674 3.2 30.9 1.0
CE1 A:HIS529 3.2 27.6 1.0
CE1 A:HIS563 3.2 23.7 1.0
OD2 A:ASP674 3.5 30.6 1.0
OD1 A:ASP564 3.6 21.9 1.0
MG A:MG802 3.7 24.9 1.0
O A:HOH929 4.0 32.2 1.0
O A:HOH972 4.0 27.5 1.0
O A:HOH939 4.0 40.6 1.0
O A:HOH1008 4.1 27.7 1.0
CD2 A:HIS525 4.2 28.4 1.0
CG A:HIS563 4.2 22.3 1.0
CG A:HIS529 4.2 27.7 1.0
ND1 A:HIS529 4.3 25.9 1.0
ND1 A:HIS563 4.3 23.3 1.0
CB A:ASP564 4.3 21.9 1.0
O A:HOH916 4.5 19.4 1.0
CB A:ASP674 4.5 28.5 1.0
NE2 A:HIS525 4.6 23.6 1.0
CG2 A:VAL533 4.8 23.0 1.0
O A:ASP674 4.9 24.0 1.0
CA A:ASP674 5.0 25.7 1.0

Zinc binding site 2 out of 4 in 5sjx

Go back to Zinc Binding Sites List in 5sjx
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.3
occ:1.00
 NE2 B:HIS529 2.1 19.0 1.0
NE2 B:HIS563 2.1 20.6 1.0
OD1 B:ASP674 2.2 21.4 1.0
O B:HOH951 2.3 14.9 1.0
OD2 B:ASP564 2.3 22.0 1.0
O B:HOH1030 2.5 30.2 1.0
CD2 B:HIS529 3.0 21.4 1.0
CG B:ASP674 3.1 21.9 1.0
CD2 B:HIS563 3.1 20.4 1.0
CE1 B:HIS529 3.1 22.6 1.0
CE1 B:HIS563 3.1 19.1 1.0
CG B:ASP564 3.2 19.2 1.0
OD2 B:ASP674 3.3 21.7 1.0
OD1 B:ASP564 3.6 23.2 1.0
MG B:MG802 3.7 15.3 1.0
O B:HOH1023 3.9 16.7 1.0
O B:HOH978 3.9 22.1 1.0
O B:HOH1027 4.1 33.9 1.0
CD2 B:HIS525 4.1 21.7 1.0
CG B:HIS529 4.2 19.9 1.0
ND1 B:HIS563 4.2 18.4 1.0
CG B:HIS563 4.2 19.9 1.0
ND1 B:HIS529 4.2 18.3 1.0
O B:HOH907 4.3 49.9 1.0
CB B:ASP564 4.3 18.2 1.0
CB B:ASP674 4.5 22.3 1.0
O B:HOH947 4.6 16.3 1.0
NE2 B:HIS525 4.7 24.8 1.0
CG2 B:VAL533 4.8 21.8 1.0
O B:ASP674 4.9 23.1 1.0
CA B:ASP674 4.9 20.3 1.0

Zinc binding site 3 out of 4 in 5sjx

Go back to Zinc Binding Sites List in 5sjx
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.2
occ:1.00
 O C:HOH955 2.1 23.9 1.0
NE2 C:HIS529 2.1 22.6 1.0
OD1 C:ASP674 2.2 20.2 1.0
OD2 C:ASP564 2.2 21.1 1.0
NE2 C:HIS563 2.2 24.6 1.0
O C:HOH976 2.6 34.3 1.0
CD2 C:HIS563 2.9 20.2 1.0
CG C:ASP674 3.0 25.2 1.0
CD2 C:HIS529 3.1 22.8 1.0
CE1 C:HIS529 3.2 22.2 1.0
CG C:ASP564 3.2 22.4 1.0
OD2 C:ASP674 3.2 27.9 1.0
CE1 C:HIS563 3.4 22.2 1.0
OD1 C:ASP564 3.6 22.5 1.0
MG C:MG802 3.8 22.4 1.0
O C:HOH1012 4.1 23.7 1.0
O C:HOH930 4.1 39.1 1.0
CD2 C:HIS525 4.1 25.8 1.0
O C:HOH1006 4.2 25.3 1.0
CG C:HIS563 4.2 21.7 1.0
O C:HOH1002 4.2 32.7 1.0
CG C:HIS529 4.2 22.2 1.0
ND1 C:HIS529 4.2 19.0 1.0
ND1 C:HIS563 4.3 23.2 1.0
CB C:ASP674 4.4 24.3 1.0
CB C:ASP564 4.4 20.8 1.0
NE2 C:HIS525 4.5 27.8 1.0
O C:HOH948 4.6 21.9 1.0
CA C:ASP674 4.8 23.6 1.0
O C:ASP674 4.8 24.3 1.0
CG2 C:VAL533 4.9 22.6 1.0
O C:HOH959 5.0 19.5 1.0

Zinc binding site 4 out of 4 in 5sjx

Go back to Zinc Binding Sites List in 5sjx
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline


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 2-[[4- (1-Methyl-4-Pyridin-4-Ylpyrazol-3-Yl)Phenoxy]Methyl]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:41.6
occ:1.00
 O D:HOH951 1.9 30.7 1.0
NE2 D:HIS563 2.0 25.9 1.0
NE2 D:HIS529 2.2 34.6 1.0
OD2 D:ASP564 2.2 40.2 1.0
OD1 D:ASP674 2.3 35.1 1.0
O D:HOH958 2.6 38.2 1.0
CD2 D:HIS563 2.8 25.1 1.0
CG D:ASP674 3.1 37.4 1.0
CE1 D:HIS529 3.1 33.6 1.0
CG D:ASP564 3.2 34.0 1.0
CD2 D:HIS529 3.2 39.2 1.0
CE1 D:HIS563 3.2 28.2 1.0
OD2 D:ASP674 3.4 35.4 1.0
OD1 D:ASP564 3.7 34.8 1.0
MG D:MG802 3.7 36.7 1.0
O D:HOH926 4.1 32.9 1.0
CG D:HIS563 4.1 25.7 1.0
O D:HOH934 4.2 29.5 1.0
ND1 D:HIS563 4.2 24.6 1.0
ND1 D:HIS529 4.2 35.2 1.0
CB D:ASP564 4.3 32.4 1.0
CD2 D:HIS525 4.3 37.4 1.0
CG D:HIS529 4.3 32.5 1.0
CB D:ASP674 4.5 37.2 1.0
O D:HOH917 4.6 27.9 1.0
NE2 D:HIS525 4.7 38.9 1.0
CG2 D:VAL533 4.7 30.9 1.0
CA D:ASP674 4.9 35.8 1.0
O D:ASP674 4.9 42.9 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 06:10:02 2024

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