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Zinc in PDB 5ske: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide, PDB code: 5ske was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.46 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.086, 135.086, 235.075, 90, 90, 120
R / Rfree (%) 17.7 / 21.5

Other elements in 5ske:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide (pdb code 5ske). 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- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide, PDB code: 5ske:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ske

Go back to Zinc Binding Sites List in 5ske
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:33.5
occ:1.00
 OD2 A:ASP564 2.0 31.3 1.0
NE2 A:HIS563 2.1 27.9 1.0
NE2 A:HIS529 2.1 31.4 1.0
OD1 A:ASP674 2.1 43.5 1.0
O A:HOH951 2.2 26.7 1.0
O A:HOH974 2.2 30.4 1.0
CD2 A:HIS563 3.0 26.8 1.0
CG A:ASP674 3.0 38.8 1.0
CD2 A:HIS529 3.1 29.5 1.0
CG A:ASP564 3.1 29.1 1.0
CE1 A:HIS563 3.1 28.2 1.0
CE1 A:HIS529 3.1 30.7 1.0
OD2 A:ASP674 3.3 38.6 1.0
OD1 A:ASP564 3.7 27.4 1.0
MG A:MG802 3.9 25.6 1.0
O A:HOH996 4.1 26.6 1.0
CG A:HIS563 4.1 27.6 1.0
ND1 A:HIS563 4.1 27.4 1.0
CD2 A:HIS525 4.2 31.2 1.0
CB A:ASP564 4.2 27.8 1.0
ND1 A:HIS529 4.2 27.8 1.0
CG A:HIS529 4.2 28.9 1.0
O A:HOH932 4.3 30.9 1.0
CB A:ASP674 4.4 34.6 1.0
NE2 A:HIS525 4.5 30.8 1.0
O A:HOH923 4.6 21.8 1.0
CG2 A:VAL533 4.7 28.2 1.0
O A:ASP674 4.8 31.8 1.0
CA A:ASP674 4.8 33.9 1.0

Zinc binding site 2 out of 4 in 5ske

Go back to Zinc Binding Sites List in 5ske
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:32.7
occ:1.00
 O B:HOH916 2.0 23.8 1.0
NE2 B:HIS563 2.1 28.7 1.0
OD1 B:ASP674 2.1 32.0 1.0
NE2 B:HIS529 2.1 26.1 1.0
O B:HOH999 2.2 30.9 1.0
OD2 B:ASP564 2.2 27.2 1.0
CG B:ASP674 3.0 33.0 1.0
CD2 B:HIS563 3.0 27.4 1.0
CE1 B:HIS563 3.1 29.6 1.0
CD2 B:HIS529 3.1 28.1 1.0
CE1 B:HIS529 3.1 28.7 1.0
CG B:ASP564 3.2 28.8 1.0
OD2 B:ASP674 3.3 29.8 1.0
OD1 B:ASP564 3.7 29.9 1.0
MG B:MG802 3.9 26.4 1.0
O B:HOH946 4.1 26.5 1.0
O B:HOH955 4.1 37.3 1.0
CG B:HIS563 4.2 27.9 1.0
ND1 B:HIS563 4.2 28.0 1.0
CD2 B:HIS525 4.2 29.2 1.0
ND1 B:HIS529 4.3 26.9 1.0
CG B:HIS529 4.3 26.8 1.0
CB B:ASP564 4.3 28.2 1.0
CB B:ASP674 4.3 32.8 1.0
NE2 B:HIS525 4.5 28.6 1.0
CG2 B:VAL533 4.6 26.9 1.0
O B:HOH941 4.7 26.6 1.0
O B:ASP674 4.7 30.6 1.0
CA B:ASP674 4.7 31.2 1.0

Zinc binding site 3 out of 4 in 5ske

Go back to Zinc Binding Sites List in 5ske
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:35.7
occ:1.00
 O C:HOH930 2.0 25.8 1.0
O C:HOH982 2.1 32.4 1.0
OD1 C:ASP674 2.1 31.4 1.0
NE2 C:HIS563 2.1 29.8 1.0
OD2 C:ASP564 2.1 29.2 1.0
NE2 C:HIS529 2.2 29.4 1.0
CG C:ASP674 3.0 32.7 1.0
CD2 C:HIS563 3.0 29.3 1.0
CD2 C:HIS529 3.1 29.6 1.0
CE1 C:HIS563 3.2 31.2 1.0
CG C:ASP564 3.2 30.1 1.0
OD2 C:ASP674 3.2 32.9 1.0
CE1 C:HIS529 3.2 30.9 1.0
OD1 C:ASP564 3.8 30.5 1.0
MG C:MG802 3.8 28.0 1.0
O C:HOH976 4.1 34.0 1.0
CD2 C:HIS525 4.1 33.8 1.0
CG C:HIS563 4.2 27.8 1.0
O C:HOH906 4.2 42.6 1.0
ND1 C:HIS563 4.2 28.1 1.0
CG C:HIS529 4.3 30.6 1.0
ND1 C:HIS529 4.3 29.3 1.0
CB C:ASP674 4.4 33.4 1.0
CB C:ASP564 4.4 29.1 1.0
NE2 C:HIS525 4.4 34.1 1.0
O C:HOH928 4.6 33.1 1.0
O C:ASP674 4.7 34.8 1.0
CG2 C:VAL533 4.7 30.4 1.0
CA C:ASP674 4.8 34.5 1.0

Zinc binding site 4 out of 4 in 5ske

Go back to Zinc Binding Sites List in 5ske
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-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 2- Tert-Butyl-5-(Pyrimidin-5-Ylamino)-N-[3-(Trifluoromethoxy) Phenyl]Pyrimidine-4-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.5
occ:1.00
 O D:HOH948 2.0 28.4 1.0
OD1 D:ASP674 2.1 39.2 1.0
NE2 D:HIS563 2.1 32.2 1.0
O D:HOH965 2.2 43.9 1.0
OD2 D:ASP564 2.2 36.6 1.0
NE2 D:HIS529 2.2 38.7 1.0
CD2 D:HIS563 2.9 34.3 1.0
CG D:ASP674 3.0 38.7 1.0
CE1 D:HIS563 3.1 32.9 1.0
CG D:ASP564 3.2 35.6 1.0
CD2 D:HIS529 3.2 37.5 1.0
CE1 D:HIS529 3.2 38.7 1.0
OD2 D:ASP674 3.3 45.8 1.0
OD1 D:ASP564 3.7 34.1 1.0
MG D:MG802 3.8 34.4 1.0
O D:HOH947 4.0 42.0 1.0
CG D:HIS563 4.1 34.3 1.0
O D:HOH958 4.2 35.9 1.0
ND1 D:HIS563 4.2 35.2 1.0
CB D:ASP564 4.3 36.4 1.0
CD2 D:HIS525 4.3 38.1 1.0
ND1 D:HIS529 4.3 38.0 1.0
CG D:HIS529 4.4 38.0 1.0
CB D:ASP674 4.4 39.6 1.0
O D:HOH919 4.4 33.0 1.0
NE2 D:HIS525 4.6 38.1 1.0
CG2 D:VAL533 4.7 40.7 1.0
O D:ASP674 4.7 34.1 1.0
CA D:ASP674 4.8 37.9 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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