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Zinc in PDB 5shr: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5shr 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 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.115, 135.115, 234.836, 90, 90, 120
R / Rfree (%) 18.2 / 23

Other elements in 5shr:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine 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 N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine (pdb code 5shr). 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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5shr:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shr

Go back to Zinc Binding Sites List in 5shr
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.8
occ:1.00
 OD2 A:ASP564 2.1 27.5 1.0
NE2 A:HIS529 2.1 30.9 1.0
O A:HOH964 2.1 27.3 1.0
NE2 A:HIS563 2.2 25.6 1.0
O A:HOH973 2.2 41.9 1.0
OD1 A:ASP674 2.3 27.9 1.0
CD2 A:HIS563 3.0 25.1 1.0
CG A:ASP564 3.1 26.6 1.0
CD2 A:HIS529 3.1 29.0 1.0
CG A:ASP674 3.1 29.7 1.0
CE1 A:HIS529 3.2 28.1 1.0
CE1 A:HIS563 3.2 29.8 1.0
OD2 A:ASP674 3.4 30.8 1.0
OD1 A:ASP564 3.6 26.3 1.0
MG A:MG802 3.8 28.7 1.0
CD2 A:HIS525 4.1 26.8 1.0
CG A:HIS563 4.2 27.2 1.0
CG A:HIS529 4.3 26.2 1.0
O A:HOH992 4.3 24.6 1.0
ND1 A:HIS529 4.3 22.6 1.0
ND1 A:HIS563 4.3 27.7 1.0
CB A:ASP564 4.3 25.2 1.0
O A:HOH944 4.4 33.8 1.0
NE2 A:HIS525 4.5 28.2 1.0
CB A:ASP674 4.5 26.5 1.0
O A:HOH927 4.5 23.4 1.0
CG2 A:VAL533 4.7 21.3 1.0
O A:ASP674 4.8 26.3 1.0
CA A:ASP674 4.9 26.2 1.0

Zinc binding site 2 out of 4 in 5shr

Go back to Zinc Binding Sites List in 5shr
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:30.2
occ:1.00
 OD2 B:ASP564 2.1 28.2 1.0
NE2 B:HIS529 2.1 21.2 1.0
O B:HOH985 2.2 21.3 1.0
NE2 B:HIS563 2.2 20.9 1.0
OD1 B:ASP674 2.2 27.1 1.0
O B:HOH923 2.7 40.2 1.0
CD2 B:HIS563 3.0 22.8 1.0
CD2 B:HIS529 3.0 26.2 1.0
CG B:ASP674 3.1 23.8 1.0
CG B:ASP564 3.1 24.5 1.0
CE1 B:HIS529 3.2 23.8 1.0
CE1 B:HIS563 3.3 24.3 1.0
OD2 B:ASP674 3.3 24.7 1.0
OD1 B:ASP564 3.6 24.1 1.0
MG B:MG802 3.8 25.4 1.0
O B:HOH1001 4.0 24.8 1.0
CD2 B:HIS525 4.1 25.8 1.0
CG B:HIS563 4.2 23.5 1.0
CG B:HIS529 4.2 24.7 1.0
ND1 B:HIS529 4.2 20.7 1.0
ND1 B:HIS563 4.3 23.3 1.0
CB B:ASP564 4.3 22.9 1.0
O B:HOH968 4.4 37.4 1.0
O B:HOH1024 4.4 47.6 1.0
NE2 B:HIS525 4.4 29.7 1.0
CB B:ASP674 4.5 26.2 1.0
O B:HOH944 4.6 28.5 1.0
CG2 B:VAL533 4.7 21.4 1.0
CA B:ASP674 4.9 23.4 1.0
O B:ASP674 4.9 27.0 1.0

Zinc binding site 3 out of 4 in 5shr

Go back to Zinc Binding Sites List in 5shr
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:32.4
occ:1.00
 NE2 C:HIS529 2.2 27.6 1.0
O C:HOH939 2.2 24.5 1.0
NE2 C:HIS563 2.2 26.7 1.0
OD2 C:ASP564 2.2 27.4 1.0
OD1 C:ASP674 2.2 23.0 1.0
O C:HOH923 2.5 43.6 1.0
CD2 C:HIS563 3.0 23.9 1.0
CD2 C:HIS529 3.0 26.1 1.0
CG C:ASP674 3.1 24.3 1.0
CG C:ASP564 3.1 24.2 1.0
OD2 C:ASP674 3.2 31.2 1.0
CE1 C:HIS563 3.3 24.1 1.0
CE1 C:HIS529 3.3 29.6 1.0
OD1 C:ASP564 3.6 24.7 1.0
MG C:MG802 3.8 27.7 1.0
CD2 C:HIS525 4.1 29.9 1.0
O C:HOH1007 4.2 20.8 1.0
CG C:HIS563 4.2 26.3 1.0
CG C:HIS529 4.2 24.4 1.0
ND1 C:HIS563 4.3 24.6 1.0
ND1 C:HIS529 4.3 26.5 1.0
CB C:ASP564 4.3 23.1 1.0
NE2 C:HIS525 4.4 29.5 1.0
O C:HOH992 4.4 49.0 1.0
O C:HOH987 4.4 36.6 1.0
CB C:ASP674 4.4 26.1 1.0
O C:HOH918 4.5 30.7 1.0
CA C:ASP674 4.8 29.5 1.0
CG2 C:VAL533 4.8 24.8 1.0
O C:ASP674 4.9 28.1 1.0

Zinc binding site 4 out of 4 in 5shr

Go back to Zinc Binding Sites List in 5shr
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine


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-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-N,2-Dimethyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.6
occ:1.00
 O D:HOH951 2.1 28.1 1.0
NE2 D:HIS563 2.2 27.1 1.0
OD2 D:ASP564 2.2 34.4 1.0
NE2 D:HIS529 2.2 29.2 1.0
OD1 D:ASP674 2.3 32.7 1.0
O D:HOH912 2.4 40.1 1.0
CD2 D:HIS563 3.0 28.5 1.0
CD2 D:HIS529 3.1 35.3 1.0
CG D:ASP564 3.1 30.7 1.0
CG D:ASP674 3.2 33.2 1.0
CE1 D:HIS529 3.3 33.6 1.0
CE1 D:HIS563 3.3 28.6 1.0
OD2 D:ASP674 3.4 36.6 1.0
OD1 D:ASP564 3.6 30.2 1.0
MG D:MG802 3.7 35.3 1.0
CD2 D:HIS525 4.0 37.5 1.0
CG D:HIS563 4.2 28.0 1.0
O D:HOH967 4.2 34.7 1.0
CB D:ASP564 4.3 33.2 1.0
CG D:HIS529 4.3 32.3 1.0
ND1 D:HIS563 4.4 28.3 1.0
ND1 D:HIS529 4.4 30.8 1.0
NE2 D:HIS525 4.4 41.0 1.0
O D:HOH961 4.5 43.1 1.0
CB D:ASP674 4.6 33.0 1.0
O D:HOH913 4.6 33.6 1.0
CG2 D:VAL533 4.7 33.6 1.0
O D:ASP674 4.8 35.4 1.0
CA D:ASP674 4.9 33.0 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 05:34:36 2024

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