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Zinc in PDB 5sjn: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sjn was solved by C.Joseph, J.Benz, A.Flohr, C.Lerner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.63 / 2.05
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.272, 135.272, 235.07, 90, 90, 120
R / Rfree (%) 18.3 / 22.7

Other elements in 5sjn:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Magnesium (Mg) 4 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine (pdb code 5sjn). 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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine, PDB code: 5sjn:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjn

Go back to Zinc Binding Sites List in 5sjn
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:32.9
occ:1.00
 O A:HOH960 2.0 36.6 1.0
OD2 A:ASP564 2.1 30.5 1.0
NE2 A:HIS563 2.1 27.3 1.0
NE2 A:HIS529 2.2 34.4 1.0
OD1 A:ASP674 2.2 30.6 1.0
O A:HOH959 2.2 31.9 1.0
CD2 A:HIS563 2.9 27.5 1.0
CD2 A:HIS529 3.1 28.6 1.0
CG A:ASP564 3.1 29.2 1.0
CG A:ASP674 3.1 33.5 1.0
CE1 A:HIS529 3.2 32.6 1.0
CE1 A:HIS563 3.2 28.2 1.0
OD2 A:ASP674 3.4 33.6 1.0
OD1 A:ASP564 3.6 27.3 1.0
MG A:MG802 3.9 29.2 1.0
CD2 A:HIS525 4.1 34.2 1.0
CG A:HIS563 4.1 28.5 1.0
O A:HOH991 4.2 27.3 1.0
ND1 A:HIS563 4.2 28.0 1.0
CG A:HIS529 4.3 33.6 1.0
ND1 A:HIS529 4.3 32.8 1.0
CB A:ASP564 4.3 25.9 1.0
NE2 A:HIS525 4.4 35.8 1.0
O A:HOH943 4.5 35.7 1.0
CB A:ASP674 4.5 29.6 1.0
O A:HOH915 4.6 24.1 1.0
CG2 A:VAL533 4.6 27.9 1.0
CA A:ASP674 4.9 27.4 1.0
O A:ASP674 4.9 30.9 1.0

Zinc binding site 2 out of 4 in 5sjn

Go back to Zinc Binding Sites List in 5sjn
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:31.4
occ:1.00
 O B:HOH945 2.1 23.6 1.0
NE2 B:HIS563 2.1 24.8 1.0
NE2 B:HIS529 2.2 22.7 1.0
OD1 B:ASP674 2.2 26.5 1.0
OD2 B:ASP564 2.2 25.3 1.0
O B:HOH952 2.3 41.5 1.0
CD2 B:HIS563 3.1 26.4 1.0
CE1 B:HIS563 3.1 23.8 1.0
CD2 B:HIS529 3.1 25.7 1.0
CG B:ASP674 3.1 30.5 1.0
CG B:ASP564 3.1 25.7 1.0
CE1 B:HIS529 3.2 25.7 1.0
OD2 B:ASP674 3.4 29.1 1.0
OD1 B:ASP564 3.5 25.8 1.0
MG B:MG802 3.7 26.1 1.0
CD2 B:HIS525 4.0 28.9 1.0
O B:HOH992 4.1 21.5 1.0
ND1 B:HIS563 4.2 26.8 1.0
CG B:HIS563 4.2 26.6 1.0
O B:HOH926 4.3 33.8 1.0
CG B:HIS529 4.3 25.6 1.0
ND1 B:HIS529 4.3 23.4 1.0
CB B:ASP564 4.4 25.9 1.0
NE2 B:HIS525 4.4 31.5 1.0
CB B:ASP674 4.5 27.9 1.0
O B:HOH935 4.6 27.6 1.0
CG2 B:VAL533 4.6 22.3 1.0
CA B:ASP674 4.9 25.8 1.0
O B:ASP674 5.0 26.7 1.0

Zinc binding site 3 out of 4 in 5sjn

Go back to Zinc Binding Sites List in 5sjn
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.5
occ:1.00
 NE2 C:HIS529 2.2 28.7 1.0
O C:HOH914 2.2 27.9 1.0
OD2 C:ASP564 2.2 30.2 1.0
OD1 C:ASP674 2.2 26.5 1.0
NE2 C:HIS563 2.3 27.5 1.0
O C:HOH940 2.5 44.3 1.0
CD2 C:HIS529 3.1 29.1 1.0
CD2 C:HIS563 3.1 24.6 1.0
CG C:ASP564 3.1 29.8 1.0
CG C:ASP674 3.1 31.7 1.0
CE1 C:HIS529 3.2 28.7 1.0
OD2 C:ASP674 3.3 35.8 1.0
CE1 C:HIS563 3.4 25.1 1.0
OD1 C:ASP564 3.5 28.3 1.0
MG C:MG802 3.7 27.6 1.0
CD2 C:HIS525 4.0 31.4 1.0
O C:HOH994 4.2 28.6 1.0
CG C:HIS529 4.3 27.8 1.0
ND1 C:HIS529 4.3 26.7 1.0
O C:HOH983 4.3 30.9 1.0
CG C:HIS563 4.3 26.5 1.0
NE2 C:HIS525 4.4 32.0 1.0
CB C:ASP564 4.4 25.1 1.0
ND1 C:HIS563 4.4 28.3 1.0
CB C:ASP674 4.5 28.3 1.0
O C:HOH1011 4.6 46.2 1.0
O C:HOH904 4.6 28.5 1.0
CG2 C:VAL533 4.8 25.9 1.0
CA C:ASP674 4.9 29.5 1.0
O C:ASP674 5.0 26.7 1.0

Zinc binding site 4 out of 4 in 5sjn

Go back to Zinc Binding Sites List in 5sjn
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine


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 6,8- Dichloro-2-[2-(6,7-Dimethyl-1H-Benzimidazol-2-Yl)Ethyl]-5-Methyl-[1, 2,4]Triazolo[1,5-A]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:39.9
occ:1.00
 O D:HOH940 1.9 29.5 1.0
NE2 D:HIS529 2.2 37.2 1.0
NE2 D:HIS563 2.2 31.3 1.0
OD1 D:ASP674 2.2 37.4 1.0
OD2 D:ASP564 2.2 35.6 1.0
O D:HOH936 2.4 46.3 1.0
CD2 D:HIS563 3.0 32.0 1.0
CG D:ASP674 3.1 36.9 1.0
CD2 D:HIS529 3.1 32.0 1.0
CG D:ASP564 3.2 34.1 1.0
CE1 D:HIS529 3.2 31.5 1.0
CE1 D:HIS563 3.3 34.2 1.0
OD2 D:ASP674 3.3 39.1 1.0
OD1 D:ASP564 3.6 35.3 1.0
MG D:MG802 3.7 35.1 1.0
O D:HOH941 4.0 36.2 1.0
CD2 D:HIS525 4.1 33.4 1.0
CG D:HIS563 4.2 32.1 1.0
ND1 D:HIS529 4.3 33.3 1.0
CG D:HIS529 4.3 30.4 1.0
ND1 D:HIS563 4.3 34.0 1.0
CB D:ASP564 4.4 30.6 1.0
O D:HOH918 4.4 43.2 1.0
CB D:ASP674 4.5 34.6 1.0
NE2 D:HIS525 4.5 41.5 1.0
O D:HOH910 4.6 29.2 1.0
CG2 D:VAL533 4.7 34.4 1.0
O D:ASP674 4.9 36.9 1.0
CA D:ASP674 4.9 33.7 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 06:02:38 2024

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