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Zinc in PDB 5sgh: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine, PDB code: 5sgh 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) 43.48 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.991, 134.991, 234.187, 90, 90, 120
R / Rfree (%) 17.7 / 22

Other elements in 5sgh:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine 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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine (pdb code 5sgh). 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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine, PDB code: 5sgh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgh

Go back to Zinc Binding Sites List in 5sgh
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine


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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.9
occ:1.00
 O A:HOH983 2.1 24.7 1.0
OD1 A:ASP674 2.1 28.1 1.0
OD2 A:ASP564 2.1 25.9 1.0
NE2 A:HIS529 2.2 28.1 1.0
NE2 A:HIS563 2.2 24.1 1.0
O A:HOH977 2.3 33.0 1.0
CG A:ASP674 3.1 29.5 1.0
CD2 A:HIS563 3.1 24.1 1.0
CG A:ASP564 3.1 25.9 1.0
CD2 A:HIS529 3.1 28.5 1.0
CE1 A:HIS529 3.2 26.3 1.0
CE1 A:HIS563 3.3 28.6 1.0
OD2 A:ASP674 3.4 32.9 1.0
OD1 A:ASP564 3.6 25.9 1.0
MG A:MG802 3.7 26.6 1.0
O A:HOH1015 4.1 29.1 1.0
CD2 A:HIS525 4.1 28.4 1.0
O A:HOH948 4.2 35.0 1.0
CG A:HIS563 4.3 26.8 1.0
CG A:HIS529 4.3 27.2 1.0
ND1 A:HIS529 4.3 26.7 1.0
CB A:ASP564 4.3 25.8 1.0
ND1 A:HIS563 4.4 27.8 1.0
NE2 A:HIS525 4.4 30.2 1.0
CB A:ASP674 4.4 25.2 1.0
O A:HOH1019 4.5 44.2 1.0
O A:HOH952 4.5 23.2 1.0
CG2 A:VAL533 4.8 21.8 1.0
CA A:ASP674 4.8 24.5 1.0
O A:ASP674 4.8 26.7 1.0

Zinc binding site 2 out of 4 in 5sgh

Go back to Zinc Binding Sites List in 5sgh
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine


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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:29.2
occ:1.00
 O B:HOH957 2.1 19.1 1.0
OD1 B:ASP674 2.1 25.4 1.0
NE2 B:HIS563 2.1 22.5 1.0
OD2 B:ASP564 2.1 24.3 1.0
NE2 B:HIS529 2.1 23.5 1.0
O B:HOH986 2.3 33.2 1.0
CG B:ASP674 3.0 26.9 1.0
CD2 B:HIS563 3.0 22.8 1.0
CD2 B:HIS529 3.1 24.4 1.0
CG B:ASP564 3.1 26.0 1.0
CE1 B:HIS529 3.2 27.3 1.0
CE1 B:HIS563 3.2 23.7 1.0
OD2 B:ASP674 3.3 27.6 1.0
OD1 B:ASP564 3.6 23.8 1.0
MG B:MG802 3.7 22.6 1.0
O B:HOH1022 3.9 23.7 1.0
CD2 B:HIS525 4.1 27.8 1.0
CG B:HIS563 4.2 23.2 1.0
O B:HOH941 4.2 35.7 1.0
ND1 B:HIS563 4.3 24.2 1.0
CG B:HIS529 4.3 23.9 1.0
ND1 B:HIS529 4.3 22.0 1.0
CB B:ASP564 4.3 23.6 1.0
CB B:ASP674 4.3 23.9 1.0
NE2 B:HIS525 4.4 29.6 1.0
O B:HOH1032 4.4 38.6 1.0
O B:HOH966 4.6 21.9 1.0
CG2 B:VAL533 4.7 23.4 1.0
CA B:ASP674 4.8 24.6 1.0
O B:ASP674 4.9 22.3 1.0

Zinc binding site 3 out of 4 in 5sgh

Go back to Zinc Binding Sites List in 5sgh
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine


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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.3
occ:1.00
 O C:HOH940 2.0 22.1 1.0
OD2 C:ASP564 2.1 24.6 1.0
NE2 C:HIS529 2.1 23.8 1.0
OD1 C:ASP674 2.1 26.1 1.0
NE2 C:HIS563 2.2 27.0 1.0
O C:HOH1019 2.2 36.2 1.0
CG C:ASP674 3.0 27.9 1.0
CD2 C:HIS563 3.0 24.5 1.0
CG C:ASP564 3.1 25.0 1.0
CD2 C:HIS529 3.1 26.9 1.0
CE1 C:HIS529 3.1 26.6 1.0
OD2 C:ASP674 3.2 33.8 1.0
CE1 C:HIS563 3.2 25.1 1.0
OD1 C:ASP564 3.5 23.5 1.0
MG C:MG802 3.7 25.4 1.0
O C:HOH1037 4.0 25.1 1.0
CD2 C:HIS525 4.1 30.1 1.0
CG C:HIS563 4.2 23.8 1.0
ND1 C:HIS529 4.3 24.8 1.0
CG C:HIS529 4.3 24.2 1.0
ND1 C:HIS563 4.3 26.4 1.0
CB C:ASP564 4.3 24.2 1.0
O C:HOH1002 4.3 37.6 1.0
CB C:ASP674 4.4 26.3 1.0
O C:HOH1014 4.4 45.0 1.0
NE2 C:HIS525 4.4 30.4 1.0
O C:HOH974 4.6 25.7 1.0
CA C:ASP674 4.8 29.1 1.0
CG2 C:VAL533 4.8 25.5 1.0
O C:ASP674 4.9 27.7 1.0
O C:HOH943 5.0 24.5 1.0

Zinc binding site 4 out of 4 in 5sgh

Go back to Zinc Binding Sites List in 5sgh
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine


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 4-[1- Methyl-6-[(1-Methyl-4-Phenylimidazol-2-Yl)Methoxy]Pyrazolo[3,4- D]Pyrimidin-4-Yl]Morpholine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:35.3
occ:1.00
 O D:HOH950 2.0 25.4 1.0
NE2 D:HIS563 2.2 25.1 1.0
NE2 D:HIS529 2.2 33.8 1.0
O D:HOH985 2.2 37.8 1.0
OD2 D:ASP564 2.2 33.6 1.0
OD1 D:ASP674 2.2 27.0 1.0
CD2 D:HIS563 2.9 27.1 1.0
CG D:ASP564 3.1 28.2 1.0
CG D:ASP674 3.1 31.6 1.0
CD2 D:HIS529 3.1 38.9 1.0
CE1 D:HIS529 3.2 33.9 1.0
OD2 D:ASP674 3.3 35.7 1.0
CE1 D:HIS563 3.3 27.2 1.0
OD1 D:ASP564 3.6 32.4 1.0
MG D:MG802 3.7 32.7 1.0
O D:HOH996 4.1 31.9 1.0
CD2 D:HIS525 4.1 38.4 1.0
CG D:HIS563 4.2 26.6 1.0
CB D:ASP564 4.2 29.6 1.0
O D:HOH941 4.3 41.4 1.0
ND1 D:HIS529 4.3 30.9 1.0
CG D:HIS529 4.3 34.5 1.0
ND1 D:HIS563 4.3 27.3 1.0
CB D:ASP674 4.4 30.2 1.0
NE2 D:HIS525 4.5 39.9 1.0
O D:HOH934 4.6 32.2 1.0
CG2 D:VAL533 4.7 35.3 1.0
O D:ASP674 4.8 28.2 1.0
CA D:ASP674 4.9 28.7 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 05:12:49 2024

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