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Zinc in PDB 5sgo: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide, PDB code: 5sgo was solved by C.Joseph, J.Benz, A.Flohr, L.Leal, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.28 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.956, 135.956, 235.68, 90, 90, 120
R / Rfree (%) 16.4 / 22.4

Other elements in 5sgo:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide (pdb code 5sgo). 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-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide, PDB code: 5sgo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgo

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide


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-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.5
occ:1.00
 O A:HOH911 1.9 35.0 1.0
NE2 A:HIS563 1.9 28.3 1.0
NE2 A:HIS529 2.0 26.9 1.0
OD2 A:ASP564 2.1 42.0 1.0
OD1 A:ASP674 2.1 46.1 1.0
CD2 A:HIS563 2.9 29.6 1.0
CD2 A:HIS529 3.0 28.4 1.0
CE1 A:HIS563 3.0 32.8 1.0
CG A:ASP674 3.1 42.1 1.0
CE1 A:HIS529 3.1 26.4 1.0
CG A:ASP564 3.1 33.2 1.0
OD2 A:ASP674 3.4 47.7 1.0
OD1 A:ASP564 3.6 34.4 1.0
CG A:HIS563 4.0 27.7 1.0
ND1 A:HIS563 4.0 28.7 1.0
O A:HOH953 4.1 48.6 1.0
CG A:HIS529 4.1 28.7 1.0
CD2 A:HIS525 4.2 37.4 1.0
ND1 A:HIS529 4.2 27.1 1.0
CB A:ASP564 4.3 33.2 1.0
CG2 A:VAL533 4.4 24.6 1.0
CB A:ASP674 4.4 37.2 1.0
O A:HOH915 4.4 41.5 1.0
NE2 A:HIS525 4.7 39.7 1.0
CA A:ASP674 4.8 33.7 1.0
O A:ASP674 4.8 32.5 1.0
O A:HOH946 5.0 38.8 1.0

Zinc binding site 2 out of 4 in 5sgo

Go back to Zinc Binding Sites List in 5sgo
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide


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-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.3
occ:1.00
 O B:HOH930 1.9 35.2 1.0
NE2 B:HIS563 2.1 25.8 1.0
NE2 B:HIS529 2.1 25.7 1.0
OD2 B:ASP564 2.1 43.6 1.0
OD1 B:ASP674 2.2 32.5 1.0
CD2 B:HIS529 2.9 28.0 1.0
CD2 B:HIS563 3.0 25.6 1.0
CE1 B:HIS563 3.1 30.8 1.0
CG B:ASP564 3.1 32.8 1.0
CE1 B:HIS529 3.1 27.1 1.0
CG B:ASP674 3.2 30.1 1.0
OD2 B:ASP674 3.5 37.4 1.0
OD1 B:ASP564 3.6 34.9 1.0
CD2 B:HIS525 4.0 33.8 1.0
CG B:HIS563 4.1 26.6 1.0
CG B:HIS529 4.1 27.4 1.0
O B:HOH958 4.2 33.3 1.0
ND1 B:HIS563 4.2 26.9 1.0
ND1 B:HIS529 4.2 27.8 1.0
CB B:ASP564 4.3 31.0 1.0
CB B:ASP674 4.5 28.6 1.0
CG2 B:VAL533 4.5 22.5 1.0
NE2 B:HIS525 4.6 33.3 1.0
O B:ASP674 4.7 30.2 1.0
CA B:ASP674 4.8 26.2 1.0

Zinc binding site 3 out of 4 in 5sgo

Go back to Zinc Binding Sites List in 5sgo
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide


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-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.0
occ:1.00
 O C:HOH924 1.9 30.6 1.0
NE2 C:HIS529 2.0 29.2 1.0
NE2 C:HIS563 2.1 26.4 1.0
OD1 C:ASP674 2.1 35.7 1.0
OD2 C:ASP564 2.2 36.0 1.0
CD2 C:HIS563 3.0 28.0 1.0
CG C:ASP674 3.0 33.4 1.0
CD2 C:HIS529 3.0 28.9 1.0
CE1 C:HIS529 3.0 34.7 1.0
CE1 C:HIS563 3.1 28.5 1.0
CG C:ASP564 3.1 32.9 1.0
OD2 C:ASP674 3.2 36.7 1.0
OD1 C:ASP564 3.7 33.1 1.0
CD2 C:HIS525 4.0 34.3 1.0
CG C:HIS563 4.2 26.9 1.0
ND1 C:HIS529 4.2 28.8 1.0
ND1 C:HIS563 4.2 27.3 1.0
CG C:HIS529 4.2 29.9 1.0
CB C:ASP564 4.3 34.2 1.0
CB C:ASP674 4.4 34.8 1.0
O C:HOH941 4.4 46.8 1.0
CG2 C:VAL533 4.5 26.5 1.0
NE2 C:HIS525 4.5 35.5 1.0
O C:HOH912 4.7 49.7 1.0
CA C:ASP674 4.8 33.9 1.0
O C:ASP674 4.9 32.1 1.0

Zinc binding site 4 out of 4 in 5sgo

Go back to Zinc Binding Sites List in 5sgo
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide


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-[3- [3-[5-(4-Fluorophenyl)Thieno[2,3-D]Pyrimidin-4- Yl]Oxypropoxy]Phenyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:41.2
occ:1.00
 O D:HOH917 2.0 37.3 1.0
NE2 D:HIS563 2.0 33.9 1.0
OD2 D:ASP564 2.1 57.7 1.0
NE2 D:HIS529 2.1 43.6 1.0
OD1 D:ASP674 2.2 53.8 1.0
CD2 D:HIS563 3.0 36.1 1.0
CE1 D:HIS563 3.1 36.0 1.0
CE1 D:HIS529 3.1 41.4 1.0
CD2 D:HIS529 3.1 45.0 1.0
CG D:ASP564 3.1 48.5 1.0
CG D:ASP674 3.2 49.7 1.0
OD2 D:ASP674 3.5 54.6 1.0
OD1 D:ASP564 3.7 50.6 1.0
CG D:HIS563 4.1 38.5 1.0
ND1 D:HIS563 4.1 38.0 1.0
ND1 D:HIS529 4.2 40.5 1.0
CD2 D:HIS525 4.2 52.4 1.0
CB D:ASP564 4.2 47.0 1.0
CG D:HIS529 4.2 41.3 1.0
O D:HOH934 4.2 44.0 1.0
CG2 D:VAL533 4.4 37.0 1.0
CB D:ASP674 4.5 47.1 1.0
NE2 D:HIS525 4.7 49.7 1.0
O D:ASP674 4.8 43.8 1.0
CA D:ASP674 4.8 46.1 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 05:16:30 2024

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