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Zinc in PDB 5skl: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide, PDB code: 5skl was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.26 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.881, 134.881, 234.277, 90, 90, 120
R / Rfree (%) 18.7 / 23.4

Other elements in 5skl:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide 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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide (pdb code 5skl). 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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide, PDB code: 5skl:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5skl

Go back to Zinc Binding Sites List in 5skl
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide


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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.7
occ:1.00
 OD2 A:ASP564 2.1 33.6 1.0
NE2 A:HIS529 2.1 33.5 1.0
NE2 A:HIS563 2.1 30.1 1.0
OD1 A:ASP674 2.1 33.4 1.0
O A:HOH967 2.2 30.4 1.0
O A:HOH975 2.3 36.1 1.0
CD2 A:HIS563 2.9 29.1 1.0
CG A:ASP674 3.0 35.7 1.0
CE1 A:HIS529 3.1 31.2 1.0
CG A:ASP564 3.1 32.2 1.0
CD2 A:HIS529 3.2 32.8 1.0
CE1 A:HIS563 3.2 32.3 1.0
OD2 A:ASP674 3.2 43.2 1.0
OD1 A:ASP564 3.6 30.0 1.0
MG A:MG802 3.8 29.5 1.0
O A:HOH987 4.1 27.7 1.0
CG A:HIS563 4.1 30.4 1.0
ND1 A:HIS529 4.2 32.2 1.0
CD2 A:HIS525 4.2 36.8 1.0
ND1 A:HIS563 4.2 30.5 1.0
CG A:HIS529 4.3 30.6 1.0
O A:HOH953 4.3 43.2 1.0
CB A:ASP564 4.3 29.7 1.0
CB A:ASP674 4.4 33.5 1.0
O A:HOH904 4.5 28.0 1.0
O A:HOH957 4.5 45.9 1.0
NE2 A:HIS525 4.5 34.5 1.0
CG2 A:VAL533 4.7 29.4 1.0
CA A:ASP674 4.8 31.7 1.0
O A:ASP674 4.9 31.4 1.0

Zinc binding site 2 out of 4 in 5skl

Go back to Zinc Binding Sites List in 5skl
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide


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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:36.0
occ:1.00
 NE2 B:HIS563 2.1 29.6 1.0
O B:HOH943 2.1 28.1 1.0
OD1 B:ASP674 2.2 36.8 1.0
NE2 B:HIS529 2.2 27.4 1.0
OD2 B:ASP564 2.2 29.0 1.0
O B:HOH959 2.5 36.5 1.0
CD2 B:HIS563 3.0 31.2 1.0
CG B:ASP674 3.0 35.6 1.0
CG B:ASP564 3.1 28.9 1.0
CD2 B:HIS529 3.1 27.6 1.0
CE1 B:HIS563 3.1 29.2 1.0
OD2 B:ASP674 3.2 36.8 1.0
CE1 B:HIS529 3.2 30.4 1.0
OD1 B:ASP564 3.5 28.8 1.0
MG B:MG802 3.8 28.5 1.0
O B:HOH980 4.0 30.6 1.0
CG B:HIS563 4.1 29.8 1.0
CD2 B:HIS525 4.1 32.0 1.0
ND1 B:HIS563 4.2 28.5 1.0
CG B:HIS529 4.3 27.9 1.0
ND1 B:HIS529 4.3 28.3 1.0
O B:HOH941 4.3 35.4 1.0
CB B:ASP564 4.4 30.0 1.0
O B:HOH991 4.4 41.0 1.0
CB B:ASP674 4.4 33.8 1.0
NE2 B:HIS525 4.4 32.8 1.0
O B:HOH920 4.5 23.9 1.0
CG2 B:VAL533 4.8 27.4 1.0
CA B:ASP674 4.9 31.1 1.0
O B:ASP674 5.0 32.3 1.0

Zinc binding site 3 out of 4 in 5skl

Go back to Zinc Binding Sites List in 5skl
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide


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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:37.2
occ:1.00
 O C:HOH936 2.0 26.5 1.0
OD1 C:ASP674 2.1 30.1 1.0
NE2 C:HIS563 2.2 27.1 1.0
NE2 C:HIS529 2.2 29.8 1.0
OD2 C:ASP564 2.2 32.2 1.0
O C:HOH994 2.4 40.1 1.0
CG C:ASP674 3.0 28.7 1.0
CD2 C:HIS563 3.0 27.1 1.0
CD2 C:HIS529 3.1 29.6 1.0
CG C:ASP564 3.2 29.5 1.0
CE1 C:HIS529 3.2 32.6 1.0
OD2 C:ASP674 3.2 32.3 1.0
CE1 C:HIS563 3.3 30.6 1.0
OD1 C:ASP564 3.6 28.8 1.0
MG C:MG802 3.8 27.8 1.0
O C:HOH992 4.1 28.7 1.0
CD2 C:HIS525 4.2 36.3 1.0
CG C:HIS563 4.2 29.7 1.0
O C:HOH948 4.3 38.5 1.0
CG C:HIS529 4.3 30.5 1.0
ND1 C:HIS529 4.3 30.7 1.0
ND1 C:HIS563 4.3 26.9 1.0
CB C:ASP564 4.4 27.5 1.0
CB C:ASP674 4.4 29.4 1.0
NE2 C:HIS525 4.4 37.9 1.0
O C:HOH997 4.5 44.0 1.0
O C:HOH938 4.5 31.5 1.0
CA C:ASP674 4.8 31.0 1.0
CG2 C:VAL533 4.8 28.9 1.0
O C:ASP674 4.9 33.8 1.0

Zinc binding site 4 out of 4 in 5skl

Go back to Zinc Binding Sites List in 5skl
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide


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 N-(6- Cyano-2-Phenylimidazo[1,2-A]Pyridin-7-Yl)-2-Methyl-4-(Morpholine-4- Carbonyl)Pyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:50.8
occ:1.00
 O D:HOH911 2.0 31.3 1.0
NE2 D:HIS563 2.2 40.3 1.0
OD2 D:ASP564 2.2 55.0 1.0
NE2 D:HIS529 2.3 43.5 1.0
OD1 D:ASP674 2.3 52.1 1.0
O D:HOH944 2.5 36.7 1.0
CD2 D:HIS563 3.0 40.0 1.0
CG D:ASP674 3.1 49.2 1.0
CG D:ASP564 3.1 45.6 1.0
CD2 D:HIS529 3.1 45.8 1.0
OD2 D:ASP674 3.2 53.2 1.0
CE1 D:HIS563 3.3 44.0 1.0
CE1 D:HIS529 3.3 44.8 1.0
OD1 D:ASP564 3.6 45.3 1.0
MG D:MG802 3.9 43.8 1.0
CD2 D:HIS525 4.1 49.3 1.0
O D:HOH934 4.1 42.3 1.0
O D:HOH949 4.1 42.6 1.0
CG D:HIS563 4.2 43.0 1.0
CB D:ASP564 4.3 48.1 1.0
ND1 D:HIS563 4.3 41.6 1.0
CG D:HIS529 4.3 44.0 1.0
ND1 D:HIS529 4.4 44.3 1.0
CB D:ASP674 4.5 50.3 1.0
O D:HOH909 4.5 48.7 1.0
NE2 D:HIS525 4.6 52.6 1.0
CG2 D:VAL533 4.7 46.7 1.0
O D:ASP674 4.8 54.8 1.0
CA D:ASP674 4.9 49.9 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 07:38:47 2024

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