Atomistry » Zinc » PDB 5ske-5slh » 5ske
Atomistry »
  Zinc »
    PDB 5ske-5slh »
      5ske »

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

Last articles

Mg in 7V2E
Mg in 7V2F
Mg in 7V2D
Mg in 7V2C
Mg in 7V1I
Mg in 7V1G
Mg in 7V1H
Mg in 7V0R
Mg in 7V09
Mg in 7V0G
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy