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Zinc in PDB 5ski: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-[(5, 8-Dimethyl-[1,2,4]Triazolo[1,5-A]Pyrazin-2-Yl)Methyl]-2-Methyl-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]-2-Methyl-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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5ski 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) 43.50 / 2.16
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.236, 135.236, 235.217, 90, 90, 120
R / Rfree (%) 17.8 / 22.8

Other elements in 5ski:

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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine (pdb code 5ski). 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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine, PDB code: 5ski:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5ski

Go back to Zinc Binding Sites List in 5ski
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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:35.4
occ:1.00
 OD2 A:ASP564 2.1 32.2 1.0
NE2 A:HIS563 2.1 26.7 1.0
NE2 A:HIS529 2.2 35.2 1.0
O A:HOH983 2.2 31.1 1.0
OD1 A:ASP674 2.3 41.7 1.0
O A:HOH942 2.4 45.8 1.0
CD2 A:HIS563 3.0 28.0 1.0
CE1 A:HIS529 3.1 30.1 1.0
CG A:ASP674 3.1 36.6 1.0
CG A:ASP564 3.2 28.5 1.0
CE1 A:HIS563 3.2 32.2 1.0
CD2 A:HIS529 3.2 33.6 1.0
OD2 A:ASP674 3.4 36.9 1.0
OD1 A:ASP564 3.6 29.8 1.0
MG A:MG802 3.8 30.5 1.0
CD2 A:HIS525 4.1 34.7 1.0
O A:HOH978 4.2 29.6 1.0
ND1 A:HIS529 4.2 28.6 1.0
CG A:HIS563 4.2 30.6 1.0
ND1 A:HIS563 4.3 29.7 1.0
CG A:HIS529 4.3 31.2 1.0
CB A:ASP564 4.4 28.6 1.0
NE2 A:HIS525 4.4 34.0 1.0
CB A:ASP674 4.5 32.5 1.0
O A:HOH970 4.6 43.9 1.0
O A:HOH917 4.6 24.1 1.0
CG2 A:VAL533 4.7 29.8 1.0
CA A:ASP674 4.8 29.6 1.0
O A:ASP674 4.9 29.7 1.0

Zinc binding site 2 out of 4 in 5ski

Go back to Zinc Binding Sites List in 5ski
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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.2
occ:1.00
 NE2 B:HIS563 2.1 28.2 1.0
NE2 B:HIS529 2.2 26.0 1.0
O B:HOH953 2.2 21.4 1.0
OD2 B:ASP564 2.2 25.7 1.0
OD1 B:ASP674 2.2 34.3 1.0
CD2 B:HIS563 3.0 29.8 1.0
CG B:ASP674 3.1 32.4 1.0
CD2 B:HIS529 3.1 30.7 1.0
CE1 B:HIS529 3.1 25.6 1.0
CE1 B:HIS563 3.2 30.3 1.0
CG B:ASP564 3.2 25.8 1.0
OD2 B:ASP674 3.4 36.4 1.0
OD1 B:ASP564 3.6 25.7 1.0
MG B:MG802 3.8 29.4 1.0
CD2 B:HIS525 4.1 31.1 1.0
O B:HOH1009 4.1 25.5 1.0
CG B:HIS563 4.2 27.3 1.0
ND1 B:HIS563 4.2 25.4 1.0
ND1 B:HIS529 4.2 25.6 1.0
CG B:HIS529 4.3 27.6 1.0
NE2 B:HIS525 4.4 32.9 1.0
CB B:ASP564 4.4 26.4 1.0
CB B:ASP674 4.5 33.2 1.0
O B:HOH944 4.5 46.0 1.0
O B:HOH957 4.6 29.4 1.0
CG2 B:VAL533 4.7 24.9 1.0
CA B:ASP674 4.8 29.8 1.0
O B:ASP674 4.9 26.9 1.0

Zinc binding site 3 out of 4 in 5ski

Go back to Zinc Binding Sites List in 5ski
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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:34.6
occ:1.00
 NE2 C:HIS529 2.1 36.6 1.0
O C:HOH952 2.1 26.6 1.0
OD1 C:ASP674 2.2 29.2 1.0
NE2 C:HIS563 2.2 28.7 1.0
OD2 C:ASP564 2.2 29.3 1.0
O C:HOH969 2.4 41.4 1.0
CD2 C:HIS563 3.0 25.5 1.0
CG C:ASP674 3.0 30.1 1.0
CD2 C:HIS529 3.0 31.4 1.0
CE1 C:HIS529 3.1 36.2 1.0
CG C:ASP564 3.2 27.9 1.0
OD2 C:ASP674 3.2 39.8 1.0
CE1 C:HIS563 3.3 26.8 1.0
OD1 C:ASP564 3.6 26.3 1.0
MG C:MG802 3.9 29.6 1.0
CD2 C:HIS525 4.0 34.0 1.0
CG C:HIS529 4.2 29.6 1.0
CG C:HIS563 4.2 29.3 1.0
ND1 C:HIS529 4.2 31.5 1.0
O C:HOH981 4.2 29.5 1.0
ND1 C:HIS563 4.3 26.6 1.0
NE2 C:HIS525 4.3 35.0 1.0
CB C:ASP674 4.4 32.3 1.0
CB C:ASP564 4.4 26.6 1.0
O C:HOH1014 4.4 59.0 1.0
O C:HOH938 4.5 27.4 1.0
O C:HOH988 4.6 45.0 1.0
CG2 C:VAL533 4.8 29.3 1.0
CA C:ASP674 4.8 34.3 1.0
O C:ASP674 4.9 34.8 1.0

Zinc binding site 4 out of 4 in 5ski

Go back to Zinc Binding Sites List in 5ski
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]-2-Methyl-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]-2-Methyl-5- Phenyl-1,2,4-Triazol-3-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.4
occ:1.00
 O D:HOH944 2.0 31.3 1.0
NE2 D:HIS563 2.2 32.9 1.0
OD2 D:ASP564 2.2 41.2 1.0
NE2 D:HIS529 2.2 37.9 1.0
OD1 D:ASP674 2.3 39.3 1.0
O D:HOH931 2.4 43.0 1.0
CD2 D:HIS563 2.9 31.3 1.0
CG D:ASP564 3.1 34.2 1.0
CG D:ASP674 3.1 38.4 1.0
CE1 D:HIS529 3.2 36.0 1.0
CD2 D:HIS529 3.2 37.2 1.0
CE1 D:HIS563 3.3 38.8 1.0
OD2 D:ASP674 3.4 42.3 1.0
OD1 D:ASP564 3.6 38.2 1.0
MG D:MG802 3.7 38.1 1.0
CD2 D:HIS525 4.0 45.1 1.0
O D:HOH926 4.1 32.6 1.0
CG D:HIS563 4.2 36.0 1.0
ND1 D:HIS529 4.3 35.3 1.0
CB D:ASP564 4.3 31.9 1.0
ND1 D:HIS563 4.3 35.6 1.0
CG D:HIS529 4.3 33.3 1.0
NE2 D:HIS525 4.4 42.3 1.0
CB D:ASP674 4.5 39.0 1.0
O D:HOH939 4.5 58.5 1.0
O D:HOH915 4.5 32.6 1.0
O D:ASP674 4.8 43.1 1.0
CG2 D:VAL533 4.8 41.0 1.0
CA D:ASP674 4.9 36.3 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

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