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Zinc in PDB 5shn: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5shn 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) 43.53 / 2.03
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.319, 135.319, 235.517, 90, 90, 120
R / Rfree (%) 18.2 / 23.4

Other elements in 5shn:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide 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 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide (pdb code 5shn). 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- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide, PDB code: 5shn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shn

Go back to Zinc Binding Sites List in 5shn
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.2
occ:1.00
 NE2 A:HIS563 2.1 24.4 1.0
OD2 A:ASP564 2.1 27.6 1.0
NE2 A:HIS529 2.2 26.1 1.0
O A:HOH953 2.2 22.6 1.0
O A:HOH997 2.2 30.8 1.0
OD1 A:ASP674 2.3 30.6 1.0
CD2 A:HIS563 3.0 20.6 1.0
CG A:ASP564 3.1 25.7 1.0
CD2 A:HIS529 3.1 24.9 1.0
CE1 A:HIS563 3.1 24.6 1.0
CG A:ASP674 3.1 32.0 1.0
CE1 A:HIS529 3.2 26.2 1.0
OD2 A:ASP674 3.3 35.7 1.0
OD1 A:ASP564 3.5 22.1 1.0
MG A:MG802 3.8 23.1 1.0
O A:HOH1009 4.1 23.0 1.0
O A:HOH963 4.1 33.9 1.0
CD2 A:HIS525 4.1 31.9 1.0
CG A:HIS563 4.2 21.8 1.0
ND1 A:HIS563 4.2 23.3 1.0
CG A:HIS529 4.2 24.5 1.0
CB A:ASP564 4.3 22.2 1.0
ND1 A:HIS529 4.3 21.4 1.0
NE2 A:HIS525 4.5 30.2 1.0
CB A:ASP674 4.5 25.6 1.0
O A:HOH962 4.7 23.4 1.0
CG2 A:VAL533 4.8 22.1 1.0
O A:ASP674 4.9 26.6 1.0
CA A:ASP674 4.9 23.4 1.0

Zinc binding site 2 out of 4 in 5shn

Go back to Zinc Binding Sites List in 5shn
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.7
occ:1.00
 O B:HOH952 2.1 29.1 1.0
O B:HOH926 2.1 18.8 1.0
OD1 B:ASP674 2.1 24.2 1.0
OD2 B:ASP564 2.1 22.0 1.0
NE2 B:HIS529 2.1 20.7 1.0
NE2 B:HIS563 2.2 20.9 1.0
CG B:ASP674 3.0 25.1 1.0
CD2 B:HIS563 3.0 22.0 1.0
CG B:ASP564 3.1 22.4 1.0
CD2 B:HIS529 3.1 23.6 1.0
CE1 B:HIS529 3.2 25.0 1.0
CE1 B:HIS563 3.2 23.0 1.0
OD2 B:ASP674 3.2 26.0 1.0
OD1 B:ASP564 3.6 22.8 1.0
MG B:MG802 3.7 21.3 1.0
O B:HOH990 4.1 32.7 1.0
O B:HOH1003 4.1 26.8 1.0
CD2 B:HIS525 4.1 27.2 1.0
CG B:HIS563 4.2 20.4 1.0
ND1 B:HIS563 4.3 19.4 1.0
CG B:HIS529 4.3 23.1 1.0
CB B:ASP564 4.3 21.0 1.0
ND1 B:HIS529 4.3 22.2 1.0
CB B:ASP674 4.3 24.3 1.0
NE2 B:HIS525 4.4 30.8 1.0
O B:HOH979 4.6 19.3 1.0
O B:HOH1029 4.6 53.0 1.0
CG2 B:VAL533 4.7 18.4 1.0
CA B:ASP674 4.8 22.0 1.0
O B:ASP674 4.8 22.9 1.0

Zinc binding site 3 out of 4 in 5shn

Go back to Zinc Binding Sites List in 5shn
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:30.6
occ:1.00
 O C:HOH931 2.0 23.5 1.0
NE2 C:HIS563 2.1 25.8 1.0
OD1 C:ASP674 2.1 26.4 1.0
OD2 C:ASP564 2.2 24.2 1.0
NE2 C:HIS529 2.2 24.4 1.0
O C:HOH1000 2.3 34.9 1.0
CD2 C:HIS563 3.0 23.7 1.0
CG C:ASP674 3.0 30.1 1.0
CD2 C:HIS529 3.1 26.4 1.0
CG C:ASP564 3.1 25.4 1.0
CE1 C:HIS529 3.2 29.2 1.0
CE1 C:HIS563 3.2 25.1 1.0
OD2 C:ASP674 3.3 31.9 1.0
OD1 C:ASP564 3.7 20.9 1.0
MG C:MG802 3.8 26.7 1.0
CD2 C:HIS525 4.0 34.4 1.0
O C:HOH1011 4.1 38.6 1.0
O C:HOH1027 4.1 25.1 1.0
CG C:HIS563 4.2 25.8 1.0
ND1 C:HIS563 4.3 22.3 1.0
CG C:HIS529 4.3 27.2 1.0
CB C:ASP564 4.3 22.7 1.0
ND1 C:HIS529 4.3 24.8 1.0
O C:HOH963 4.3 49.5 1.0
CB C:ASP674 4.4 31.3 1.0
NE2 C:HIS525 4.4 33.0 1.0
O C:HOH932 4.5 30.0 1.0
CG2 C:VAL533 4.7 25.5 1.0
CA C:ASP674 4.7 26.2 1.0
O C:ASP674 4.8 23.1 1.0

Zinc binding site 4 out of 4 in 5shn

Go back to Zinc Binding Sites List in 5shn
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide


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- Methyl-4-N-(1,3-Oxazol-2-Ylmethyl)-3-N-(2-Phenylimidazo[1,2- A]Pyrimidin-7-Yl)Pyrazole-3,4-Dicarboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.5
occ:1.00
 O D:HOH918 2.1 21.1 1.0
NE2 D:HIS563 2.1 22.4 1.0
NE2 D:HIS529 2.1 35.4 1.0
O D:HOH986 2.1 38.1 1.0
OD2 D:ASP564 2.2 33.3 1.0
OD1 D:ASP674 2.3 30.9 1.0
CD2 D:HIS563 2.9 28.7 1.0
CD2 D:HIS529 3.0 35.4 1.0
CG D:ASP564 3.1 29.7 1.0
CE1 D:HIS529 3.1 35.8 1.0
CG D:ASP674 3.1 33.2 1.0
CE1 D:HIS563 3.2 26.9 1.0
OD2 D:ASP674 3.3 35.6 1.0
OD1 D:ASP564 3.6 29.4 1.0
MG D:MG802 3.9 31.2 1.0
O D:HOH960 4.1 38.3 1.0
CG D:HIS563 4.1 25.2 1.0
O D:HOH980 4.1 29.2 1.0
ND1 D:HIS529 4.2 30.6 1.0
CG D:HIS529 4.2 33.0 1.0
CB D:ASP564 4.2 29.3 1.0
CD2 D:HIS525 4.2 34.4 1.0
ND1 D:HIS563 4.2 28.2 1.0
CB D:ASP674 4.5 30.9 1.0
O D:HOH930 4.6 30.2 1.0
NE2 D:HIS525 4.6 40.4 1.0
CG2 D:VAL533 4.6 34.6 1.0
O D:ASP674 4.7 31.3 1.0
CA D:ASP674 4.8 31.7 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 05:34:35 2024

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