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Zinc in PDB 5sjg: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One, PDB code: 5sjg 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) 43.58 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.482, 135.482, 235.361, 90, 90, 120
R / Rfree (%) 17.6 / 22.4

Other elements in 5sjg:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One 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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One (pdb code 5sjg). 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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One, PDB code: 5sjg:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjg

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:28.4
occ:1.00
 OD2 A:ASP564 2.1 26.6 1.0
NE2 A:HIS529 2.1 23.8 1.0
O A:HOH983 2.1 25.0 1.0
OD1 A:ASP674 2.2 25.3 1.0
O A:HOH982 2.2 40.0 1.0
NE2 A:HIS563 2.2 21.6 1.0
CD2 A:HIS563 3.0 21.2 1.0
CG A:ASP564 3.1 23.0 1.0
CG A:ASP674 3.1 26.2 1.0
CD2 A:HIS529 3.1 25.6 1.0
CE1 A:HIS529 3.1 24.3 1.0
CE1 A:HIS563 3.3 28.3 1.0
OD2 A:ASP674 3.4 29.2 1.0
OD1 A:ASP564 3.6 24.1 1.0
MG A:MG802 3.9 24.4 1.0
CD2 A:HIS525 4.0 28.5 1.0
O A:HOH1010 4.2 19.4 1.0
CG A:HIS563 4.2 22.5 1.0
ND1 A:HIS529 4.2 23.0 1.0
CG A:HIS529 4.3 25.7 1.0
CB A:ASP564 4.3 23.9 1.0
ND1 A:HIS563 4.3 25.0 1.0
NE2 A:HIS525 4.4 27.9 1.0
CB A:ASP674 4.4 24.1 1.0
O A:HOH923 4.5 22.0 1.0
CG2 A:VAL533 4.6 21.9 1.0
O A:HOH954 4.7 37.4 1.0
CA A:ASP674 4.8 23.1 1.0
O A:ASP674 4.9 25.1 1.0

Zinc binding site 2 out of 4 in 5sjg

Go back to Zinc Binding Sites List in 5sjg
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.8
occ:1.00
 NE2 B:HIS563 2.1 20.8 1.0
OD1 B:ASP674 2.1 22.4 1.0
O B:HOH974 2.1 19.8 1.0
OD2 B:ASP564 2.1 21.5 1.0
NE2 B:HIS529 2.2 19.8 1.0
O B:HOH962 2.6 45.6 1.0
CD2 B:HIS563 3.0 22.1 1.0
CG B:ASP674 3.0 25.7 1.0
CD2 B:HIS529 3.1 24.1 1.0
CE1 B:HIS563 3.1 22.1 1.0
CG B:ASP564 3.1 21.4 1.0
OD2 B:ASP674 3.3 24.3 1.0
CE1 B:HIS529 3.3 23.2 1.0
OD1 B:ASP564 3.6 22.0 1.0
MG B:MG802 3.8 23.6 1.0
CD2 B:HIS525 4.0 24.7 1.0
CG B:HIS563 4.1 23.2 1.0
O B:HOH1002 4.2 21.5 1.0
ND1 B:HIS563 4.2 22.1 1.0
CG B:HIS529 4.3 22.1 1.0
CB B:ASP564 4.3 20.8 1.0
ND1 B:HIS529 4.4 20.1 1.0
NE2 B:HIS525 4.4 28.1 1.0
CB B:ASP674 4.4 24.5 1.0
O B:HOH965 4.5 42.0 1.0
O B:HOH915 4.6 22.0 1.0
CG2 B:VAL533 4.6 20.0 1.0
CA B:ASP674 4.9 23.6 1.0
O B:ASP674 5.0 23.6 1.0

Zinc binding site 3 out of 4 in 5sjg

Go back to Zinc Binding Sites List in 5sjg
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:28.2
occ:1.00
 O C:HOH970 2.1 21.8 1.0
OD2 C:ASP564 2.1 25.2 1.0
NE2 C:HIS529 2.1 24.6 1.0
OD1 C:ASP674 2.2 26.0 1.0
NE2 C:HIS563 2.2 21.4 1.0
O C:HOH972 2.5 36.5 1.0
CD2 C:HIS563 3.0 20.9 1.0
CD2 C:HIS529 3.1 23.4 1.0
CG C:ASP564 3.1 23.9 1.0
CG C:ASP674 3.1 26.1 1.0
CE1 C:HIS529 3.2 25.8 1.0
CE1 C:HIS563 3.3 20.7 1.0
OD2 C:ASP674 3.4 32.1 1.0
OD1 C:ASP564 3.6 21.7 1.0
MG C:MG802 3.8 22.9 1.0
CD2 C:HIS525 4.0 26.4 1.0
CG C:HIS529 4.2 26.2 1.0
CG C:HIS563 4.2 22.7 1.0
O C:HOH1016 4.3 20.6 1.0
ND1 C:HIS529 4.3 23.0 1.0
CB C:ASP564 4.3 22.1 1.0
NE2 C:HIS525 4.3 27.2 1.0
ND1 C:HIS563 4.4 21.4 1.0
O C:HOH1000 4.4 37.3 1.0
CB C:ASP674 4.5 26.7 1.0
O C:HOH961 4.6 27.7 1.0
CG2 C:VAL533 4.7 21.5 1.0
CA C:ASP674 4.8 25.6 1.0
O C:ASP674 5.0 28.1 1.0

Zinc binding site 4 out of 4 in 5sjg

Go back to Zinc Binding Sites List in 5sjg
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One


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 1-[2- [2-(5,8-Dimethyl-[1,2,4]Triazolo[1,5-C]Pyrimidin-2-Yl)Ethyl]-1- Methylimidazol-4-Yl]Pyrrolidin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.9
occ:1.00
 O D:HOH951 2.0 22.6 1.0
NE2 D:HIS563 2.1 24.1 1.0
O D:HOH947 2.1 39.2 1.0
NE2 D:HIS529 2.1 33.2 1.0
OD2 D:ASP564 2.1 36.8 1.0
OD1 D:ASP674 2.3 30.0 1.0
CD2 D:HIS563 2.9 26.8 1.0
CE1 D:HIS529 3.1 33.2 1.0
CD2 D:HIS529 3.1 34.4 1.0
CG D:ASP564 3.1 30.5 1.0
CG D:ASP674 3.1 31.0 1.0
CE1 D:HIS563 3.2 28.1 1.0
OD2 D:ASP674 3.3 32.1 1.0
OD1 D:ASP564 3.6 30.8 1.0
MG D:MG802 3.7 34.1 1.0
CD2 D:HIS525 4.1 32.2 1.0
CG D:HIS563 4.2 25.2 1.0
ND1 D:HIS529 4.2 33.1 1.0
O D:HOH974 4.2 24.0 1.0
CG D:HIS529 4.3 32.0 1.0
ND1 D:HIS563 4.3 25.6 1.0
CB D:ASP564 4.3 30.8 1.0
NE2 D:HIS525 4.4 37.8 1.0
O D:HOH905 4.5 42.5 1.0
O D:HOH938 4.5 29.9 1.0
CB D:ASP674 4.5 31.0 1.0
CG2 D:VAL533 4.7 33.6 1.0
O D:ASP674 4.9 32.8 1.0
CA D:ASP674 4.9 29.1 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 06:00:32 2024

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