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Zinc in PDB 5shc: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide, PDB code: 5shc was solved by C.Joseph, J.Benz, A.Flohr, M.Koerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.55 / 2.33
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.409, 135.409, 234.936, 90, 90, 120
R / Rfree (%) 17.8 / 22.5

Other elements in 5shc:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide (pdb code 5shc). 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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide, PDB code: 5shc:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shc

Go back to Zinc Binding Sites List in 5shc
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.3
occ:1.00
 OD2 A:ASP564 2.0 37.3 1.0
NE2 A:HIS563 2.1 31.4 1.0
NE2 A:HIS529 2.1 38.4 1.0
OD1 A:ASP674 2.1 49.8 1.0
O A:HOH917 2.2 28.4 1.0
O A:HOH955 2.2 39.8 1.0
CD2 A:HIS563 3.0 34.1 1.0
CG A:ASP674 3.0 47.0 1.0
CE1 A:HIS529 3.0 39.3 1.0
CG A:ASP564 3.1 34.5 1.0
CD2 A:HIS529 3.1 39.5 1.0
CE1 A:HIS563 3.1 35.8 1.0
OD2 A:ASP674 3.2 54.4 1.0
OD1 A:ASP564 3.7 32.4 1.0
MG A:MG802 3.9 33.7 1.0
O A:HOH924 4.1 40.2 1.0
CD2 A:HIS525 4.1 40.6 1.0
CG A:HIS563 4.1 32.5 1.0
ND1 A:HIS529 4.1 38.9 1.0
ND1 A:HIS563 4.2 32.6 1.0
CG A:HIS529 4.2 38.0 1.0
CB A:ASP564 4.2 33.3 1.0
O A:HOH961 4.2 32.7 1.0
CB A:ASP674 4.4 42.1 1.0
NE2 A:HIS525 4.5 41.5 1.0
O A:HOH909 4.6 35.4 1.0
CG2 A:VAL533 4.7 34.6 1.0
O A:ASP674 4.8 40.0 1.0
CA A:ASP674 4.8 38.4 1.0

Zinc binding site 2 out of 4 in 5shc

Go back to Zinc Binding Sites List in 5shc
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:40.8
occ:1.00
 OD2 B:ASP564 2.1 38.1 1.0
NE2 B:HIS563 2.1 34.9 1.0
OD1 B:ASP674 2.1 38.3 1.0
NE2 B:HIS529 2.2 35.0 1.0
O B:HOH929 2.2 26.7 1.0
O B:HOH959 2.2 42.0 1.0
CG B:ASP674 3.0 38.7 1.0
CD2 B:HIS563 3.0 33.5 1.0
CD2 B:HIS529 3.1 36.0 1.0
CG B:ASP564 3.1 35.0 1.0
CE1 B:HIS563 3.1 35.1 1.0
CE1 B:HIS529 3.2 36.4 1.0
OD2 B:ASP674 3.3 41.7 1.0
OD1 B:ASP564 3.6 32.1 1.0
MG B:MG802 3.9 34.3 1.0
O B:HOH968 3.9 31.6 1.0
CD2 B:HIS525 4.2 42.2 1.0
CG B:HIS563 4.2 34.5 1.0
ND1 B:HIS563 4.2 34.0 1.0
O B:HOH961 4.2 46.7 1.0
CG B:HIS529 4.3 35.0 1.0
CB B:ASP564 4.3 32.5 1.0
ND1 B:HIS529 4.3 37.6 1.0
CB B:ASP674 4.4 38.3 1.0
NE2 B:HIS525 4.5 40.9 1.0
O B:HOH924 4.6 33.8 1.0
CG2 B:VAL533 4.7 31.2 1.0
O B:ASP674 4.8 36.6 1.0
CA B:ASP674 4.8 36.1 1.0

Zinc binding site 3 out of 4 in 5shc

Go back to Zinc Binding Sites List in 5shc
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:43.0
occ:1.00
 O C:HOH928 2.0 28.1 1.0
OD2 C:ASP564 2.0 39.0 1.0
NE2 C:HIS529 2.1 40.3 1.0
OD1 C:ASP674 2.2 38.3 1.0
NE2 C:HIS563 2.2 37.6 1.0
O C:HOH957 2.2 39.7 1.0
CD2 C:HIS563 3.0 33.1 1.0
CG C:ASP674 3.0 36.4 1.0
CD2 C:HIS529 3.1 38.2 1.0
CG C:ASP564 3.1 36.1 1.0
CE1 C:HIS529 3.1 39.9 1.0
OD2 C:ASP674 3.2 37.5 1.0
CE1 C:HIS563 3.3 37.0 1.0
OD1 C:ASP564 3.6 37.6 1.0
MG C:MG802 3.9 32.6 1.0
CD2 C:HIS525 4.1 38.7 1.0
CG C:HIS563 4.2 33.6 1.0
O C:HOH960 4.2 41.6 1.0
O C:HOH966 4.2 35.5 1.0
CG C:HIS529 4.2 35.5 1.0
ND1 C:HIS529 4.2 38.9 1.0
CB C:ASP564 4.3 35.5 1.0
ND1 C:HIS563 4.3 32.9 1.0
CB C:ASP674 4.4 37.7 1.0
NE2 C:HIS525 4.4 40.6 1.0
O C:HOH934 4.7 36.1 1.0
CA C:ASP674 4.8 38.4 1.0
CG2 C:VAL533 4.8 31.6 1.0
O C:ASP674 4.8 39.3 1.0

Zinc binding site 4 out of 4 in 5shc

Go back to Zinc Binding Sites List in 5shc
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-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 1-[2- (5-Methyl-2-Phenyl-1,3-Oxazol-4-Yl)Ethyl]-2-Oxo-N-Pyrimidin-5- Ylpyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:56.6
occ:1.00
 NE2 D:HIS563 2.1 45.7 1.0
OD2 D:ASP564 2.1 62.7 1.0
OD1 D:ASP674 2.1 69.5 1.0
NE2 D:HIS529 2.2 53.7 1.0
O D:HOH910 2.3 36.9 1.0
O D:HOH911 2.4 46.1 1.0
CD2 D:HIS563 3.0 46.2 1.0
CG D:ASP674 3.1 58.7 1.0
CG D:ASP564 3.1 56.1 1.0
CD2 D:HIS529 3.2 52.5 1.0
CE1 D:HIS563 3.2 49.1 1.0
CE1 D:HIS529 3.3 52.3 1.0
OD2 D:ASP674 3.4 61.0 1.0
OD1 D:ASP564 3.7 57.7 1.0
MG D:MG802 3.9 54.3 1.0
CD2 D:HIS525 4.1 62.6 1.0
CG D:HIS563 4.2 47.0 1.0
ND1 D:HIS563 4.2 47.6 1.0
CB D:ASP564 4.2 54.3 1.0
CG D:HIS529 4.3 50.0 1.0
ND1 D:HIS529 4.3 51.9 1.0
CB D:ASP674 4.4 55.9 1.0
NE2 D:HIS525 4.4 65.7 1.0
O D:HOH901 4.7 40.9 1.0
O D:ASP674 4.7 61.7 1.0
CG2 D:VAL533 4.8 53.0 1.0
CA D:ASP674 4.8 54.6 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 05:27:06 2024

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