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Zinc in PDB 5sib: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sib was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.54
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.556, 135.556, 235.636, 90, 90, 120
R / Rfree (%) 17.2 / 24.9

Other elements in 5sib:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Fluorine (F) 12 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine (pdb code 5sib). 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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine, PDB code: 5sib:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sib

Go back to Zinc Binding Sites List in 5sib
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:45.5
occ:1.00
 OD2 A:ASP564 2.0 46.2 1.0
O A:HOH942 2.1 34.7 1.0
OD1 A:ASP674 2.1 40.0 1.0
NE2 A:HIS529 2.1 42.4 1.0
NE2 A:HIS563 2.1 32.6 1.0
O A:HOH940 2.3 36.8 1.0
CG A:ASP674 3.0 38.0 1.0
CD2 A:HIS529 3.0 46.3 1.0
CD2 A:HIS563 3.0 35.6 1.0
CG A:ASP564 3.1 40.9 1.0
CE1 A:HIS563 3.1 35.2 1.0
CE1 A:HIS529 3.2 38.4 1.0
OD2 A:ASP674 3.3 37.4 1.0
OD1 A:ASP564 3.6 44.6 1.0
MG A:MG802 3.7 37.9 1.0
CD2 A:HIS525 4.1 38.1 1.0
O A:HOH932 4.1 43.2 1.0
O A:HOH961 4.1 34.8 1.0
CG A:HIS563 4.2 34.4 1.0
ND1 A:HIS563 4.2 32.7 1.0
CG A:HIS529 4.2 40.0 1.0
ND1 A:HIS529 4.2 42.7 1.0
CB A:ASP564 4.3 34.9 1.0
NE2 A:HIS525 4.4 36.5 1.0
CB A:ASP674 4.4 37.9 1.0
O A:HOH910 4.6 31.4 1.0
CG2 A:VAL533 4.8 32.4 1.0
CA A:ASP674 4.9 35.5 1.0
O A:ASP674 4.9 39.7 1.0

Zinc binding site 2 out of 4 in 5sib

Go back to Zinc Binding Sites List in 5sib
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.8
occ:1.00
 NE2 B:HIS563 2.1 35.2 1.0
OD1 B:ASP674 2.1 37.3 1.0
NE2 B:HIS529 2.1 28.9 1.0
O B:HOH952 2.1 23.3 1.0
OD2 B:ASP564 2.2 44.4 1.0
O B:HOH938 2.2 28.9 1.0
CG B:ASP674 3.0 36.5 1.0
CD2 B:HIS563 3.1 37.0 1.0
CD2 B:HIS529 3.1 30.2 1.0
CE1 B:HIS563 3.1 42.2 1.0
CE1 B:HIS529 3.2 29.9 1.0
CG B:ASP564 3.2 39.2 1.0
OD2 B:ASP674 3.4 35.1 1.0
OD1 B:ASP564 3.7 39.9 1.0
MG B:MG802 3.9 33.8 1.0
O B:HOH961 4.0 30.4 1.0
O B:HOH944 4.1 31.3 1.0
CD2 B:HIS525 4.2 38.3 1.0
CG B:HIS563 4.2 33.9 1.0
CG B:HIS529 4.2 31.6 1.0
ND1 B:HIS529 4.2 31.0 1.0
ND1 B:HIS563 4.2 35.5 1.0
CB B:ASP674 4.4 37.6 1.0
NE2 B:HIS525 4.4 35.0 1.0
CB B:ASP564 4.4 37.2 1.0
O B:HOH918 4.5 36.6 1.0
CG2 B:VAL533 4.7 35.9 1.0
O B:ASP674 4.8 37.5 1.0
CA B:ASP674 4.8 32.8 1.0

Zinc binding site 3 out of 4 in 5sib

Go back to Zinc Binding Sites List in 5sib
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:44.8
occ:1.00
 OD2 C:ASP564 2.0 49.4 1.0
NE2 C:HIS563 2.1 39.4 1.0
OD1 C:ASP674 2.1 39.5 1.0
O C:HOH946 2.1 39.1 1.0
O C:HOH929 2.2 24.9 1.0
NE2 C:HIS529 2.2 36.2 1.0
CD2 C:HIS563 3.0 37.8 1.0
CG C:ASP674 3.0 33.2 1.0
CD2 C:HIS529 3.1 35.9 1.0
CG C:ASP564 3.1 42.2 1.0
CE1 C:HIS563 3.1 39.0 1.0
OD2 C:ASP674 3.3 35.9 1.0
CE1 C:HIS529 3.3 37.8 1.0
OD1 C:ASP564 3.7 39.1 1.0
MG C:MG802 3.8 35.9 1.0
O C:HOH923 4.1 36.9 1.0
CD2 C:HIS525 4.1 48.4 1.0
CG C:HIS563 4.2 37.4 1.0
O C:HOH960 4.2 22.9 1.0
ND1 C:HIS563 4.2 35.0 1.0
CB C:ASP564 4.2 39.8 1.0
CG C:HIS529 4.3 34.5 1.0
O C:HOH969 4.3 45.0 1.0
ND1 C:HIS529 4.4 33.7 1.0
NE2 C:HIS525 4.4 47.8 1.0
CB C:ASP674 4.4 34.7 1.0
O C:HOH940 4.6 31.3 1.0
CG2 C:VAL533 4.9 40.0 1.0
CA C:ASP674 4.9 36.6 1.0

Zinc binding site 4 out of 4 in 5sib

Go back to Zinc Binding Sites List in 5sib
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine


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 3- Methyl-6-[2-(2-Methyl-5-Pyrrolidin-1-Yl-1,2,4-Triazol-3-Yl)Ethyl]-2- (Trifluoromethyl)Imidazo[1,2-B]Pyridazine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:67.3
occ:1.00
 OD2 D:ASP564 1.9 69.1 1.0
OD1 D:ASP674 2.1 62.0 1.0
O D:HOH918 2.1 38.0 1.0
NE2 D:HIS563 2.2 50.2 1.0
O D:HOH907 2.3 43.1 1.0
NE2 D:HIS529 2.3 55.2 1.0
CD2 D:HIS563 3.0 50.6 1.0
CG D:ASP564 3.1 67.1 1.0
CG D:ASP674 3.1 62.5 1.0
CD2 D:HIS529 3.1 57.8 1.0
CE1 D:HIS563 3.2 54.3 1.0
CE1 D:HIS529 3.4 58.0 1.0
OD2 D:ASP674 3.4 61.7 1.0
OD1 D:ASP564 3.7 63.0 1.0
MG D:MG802 3.9 49.4 1.0
O D:HOH915 4.0 47.3 1.0
CD2 D:HIS525 4.0 63.7 1.0
O D:HOH902 4.1 49.1 1.0
CG D:HIS563 4.2 54.7 1.0
ND1 D:HIS563 4.3 52.4 1.0
CB D:ASP564 4.3 63.1 1.0
NE2 D:HIS525 4.3 68.6 1.0
CG D:HIS529 4.3 50.8 1.0
ND1 D:HIS529 4.4 59.2 1.0
CB D:ASP674 4.4 67.6 1.0
O D:HOH906 4.5 47.4 1.0
O D:ASP674 4.7 71.7 1.0
CG2 D:VAL533 4.8 61.2 1.0
CA D:ASP674 4.9 68.6 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 05:45:11 2024

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