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Zinc in PDB 5sgx: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sgx 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) 43.72 / 1.93
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.599, 135.599, 235.562, 90, 90, 120
R / Rfree (%) 16.8 / 21.6

Other elements in 5sgx:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine also contains other interesting chemical elements:

Fluorine (F) 12 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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine (pdb code 5sgx). 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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine, PDB code: 5sgx:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgx

Go back to Zinc Binding Sites List in 5sgx
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.7
occ:1.00
 O A:HOH988 2.1 24.8 1.0
NE2 A:HIS529 2.1 24.9 1.0
OD2 A:ASP564 2.2 25.9 1.0
OD1 A:ASP674 2.2 27.7 1.0
NE2 A:HIS563 2.2 23.8 1.0
O A:HOH994 2.3 38.4 1.0
CD2 A:HIS563 3.1 21.8 1.0
CD2 A:HIS529 3.1 24.1 1.0
CG A:ASP674 3.1 28.8 1.0
CG A:ASP564 3.1 25.7 1.0
CE1 A:HIS529 3.2 24.7 1.0
CE1 A:HIS563 3.3 27.4 1.0
OD2 A:ASP674 3.5 30.6 1.0
OD1 A:ASP564 3.6 23.1 1.0
MG A:MG802 3.8 26.9 1.0
CD2 A:HIS525 4.0 27.7 1.0
CG A:HIS563 4.2 22.9 1.0
O A:HOH1031 4.2 23.5 1.0
CG A:HIS529 4.3 26.1 1.0
ND1 A:HIS529 4.3 21.7 1.0
ND1 A:HIS563 4.3 24.9 1.0
CB A:ASP564 4.4 25.4 1.0
NE2 A:HIS525 4.4 28.7 1.0
CB A:ASP674 4.4 24.2 1.0
O A:HOH962 4.6 35.8 1.0
O A:HOH934 4.6 23.3 1.0
CG2 A:VAL533 4.7 25.2 1.0
CA A:ASP674 4.9 25.4 1.0
O A:ASP674 4.9 24.6 1.0

Zinc binding site 2 out of 4 in 5sgx

Go back to Zinc Binding Sites List in 5sgx
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:27.5
occ:1.00
 NE2 B:HIS563 2.1 22.2 1.0
O B:HOH970 2.1 20.6 1.0
OD1 B:ASP674 2.1 25.1 1.0
NE2 B:HIS529 2.2 20.6 1.0
OD2 B:ASP564 2.2 20.4 1.0
O B:HOH922 2.4 42.1 1.0
CD2 B:HIS563 3.0 21.8 1.0
CG B:ASP674 3.0 28.2 1.0
CD2 B:HIS529 3.1 24.4 1.0
CG B:ASP564 3.1 20.9 1.0
CE1 B:HIS563 3.2 22.4 1.0
CE1 B:HIS529 3.2 23.3 1.0
OD2 B:ASP674 3.3 27.3 1.0
OD1 B:ASP564 3.6 23.5 1.0
MG B:MG802 3.7 23.9 1.0
CD2 B:HIS525 4.0 24.5 1.0
O B:HOH1019 4.1 22.2 1.0
CG B:HIS563 4.2 20.8 1.0
ND1 B:HIS563 4.3 19.6 1.0
CG B:HIS529 4.3 21.3 1.0
ND1 B:HIS529 4.3 20.3 1.0
NE2 B:HIS525 4.3 32.0 1.0
CB B:ASP564 4.3 22.2 1.0
O B:HOH966 4.4 44.6 1.0
CB B:ASP674 4.4 24.2 1.0
O B:HOH933 4.6 24.0 1.0
CG2 B:VAL533 4.7 20.8 1.0
CA B:ASP674 4.8 21.0 1.0
O B:ASP674 4.9 22.3 1.0

Zinc binding site 3 out of 4 in 5sgx

Go back to Zinc Binding Sites List in 5sgx
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.5
occ:1.00
 O C:HOH923 2.0 22.5 1.0
NE2 C:HIS529 2.1 22.4 1.0
OD2 C:ASP564 2.2 24.7 1.0
OD1 C:ASP674 2.2 23.7 1.0
NE2 C:HIS563 2.2 23.9 1.0
O C:HOH967 2.4 40.2 1.0
CG C:ASP674 3.0 26.1 1.0
CD2 C:HIS529 3.1 24.0 1.0
CD2 C:HIS563 3.1 24.0 1.0
CE1 C:HIS529 3.1 25.1 1.0
CG C:ASP564 3.2 24.8 1.0
CE1 C:HIS563 3.2 22.1 1.0
OD2 C:ASP674 3.2 32.0 1.0
OD1 C:ASP564 3.6 26.5 1.0
MG C:MG802 3.8 25.1 1.0
CD2 C:HIS525 4.0 27.5 1.0
CG C:HIS529 4.2 23.0 1.0
ND1 C:HIS529 4.2 20.6 1.0
CG C:HIS563 4.2 22.8 1.0
O C:HOH1052 4.3 23.3 1.0
ND1 C:HIS563 4.3 24.1 1.0
NE2 C:HIS525 4.3 28.1 1.0
CB C:ASP564 4.3 24.2 1.0
CB C:ASP674 4.4 22.4 1.0
O C:HOH986 4.5 42.1 1.0
O C:HOH956 4.5 24.4 1.0
CG2 C:VAL533 4.7 22.9 1.0
CA C:ASP674 4.8 24.1 1.0
O C:ASP674 5.0 25.9 1.0

Zinc binding site 4 out of 4 in 5sgx

Go back to Zinc Binding Sites List in 5sgx
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine


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 5,8- Dimethyl-2-[2-[2-Methyl-5-[(2R)-2-(Trifluoromethyl)Pyrrolidin-1-Yl]- 1,2,4-Triazol-3-Yl]Ethyl]-[1,2,4]Triazolo[1,5-C]Pyrimidine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:34.3
occ:1.00
 O D:HOH938 2.0 25.9 1.0
NE2 D:HIS563 2.1 28.2 1.0
NE2 D:HIS529 2.1 31.9 1.0
OD2 D:ASP564 2.2 33.8 1.0
O D:HOH955 2.2 41.4 1.0
OD1 D:ASP674 2.3 29.8 1.0
CD2 D:HIS563 2.9 31.4 1.0
CG D:ASP674 3.1 27.5 1.0
CD2 D:HIS529 3.1 32.5 1.0
CG D:ASP564 3.1 28.5 1.0
CE1 D:HIS529 3.1 31.9 1.0
OD2 D:ASP674 3.3 34.2 1.0
CE1 D:HIS563 3.3 28.8 1.0
OD1 D:ASP564 3.6 30.6 1.0
MG D:MG802 3.8 34.2 1.0
CD2 D:HIS525 4.0 35.7 1.0
CG D:HIS563 4.2 27.7 1.0
ND1 D:HIS529 4.2 31.9 1.0
O D:HOH942 4.2 27.0 1.0
CG D:HIS529 4.3 30.4 1.0
ND1 D:HIS563 4.3 29.8 1.0
CB D:ASP564 4.3 29.8 1.0
NE2 D:HIS525 4.4 40.5 1.0
O D:HOH957 4.4 44.5 1.0
CB D:ASP674 4.5 29.7 1.0
O D:HOH920 4.5 30.9 1.0
CG2 D:VAL533 4.7 32.6 1.0
O D:ASP674 4.8 32.3 1.0
CA D:ASP674 4.9 27.9 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 05:20:15 2024

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