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Zinc in PDB 5sgi: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine, PDB code: 5sgi was solved by C.Joseph, J.Benz, A.Flohr, M.Brunner, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.63 / 1.97
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.86, 135.86, 235.3, 90, 90, 120
R / Rfree (%) 18.2 / 23.5

Other elements in 5sgi:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine 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 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine (pdb code 5sgi). 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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine, PDB code: 5sgi:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgi

Go back to Zinc Binding Sites List in 5sgi
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:27.3
occ:1.00
 NE2 A:HIS563 2.1 23.1 1.0
OD1 A:ASP674 2.1 23.8 1.0
NE2 A:HIS529 2.2 20.2 1.0
OD2 A:ASP564 2.2 24.4 1.0
CD2 A:HIS563 3.0 21.3 1.0
CD2 A:HIS529 3.1 21.6 1.0
CG A:ASP674 3.1 24.4 1.0
CE1 A:HIS563 3.1 25.4 1.0
CG A:ASP564 3.2 23.9 1.0
CE1 A:HIS529 3.2 22.5 1.0
OD2 A:ASP674 3.4 28.7 1.0
OD1 A:ASP564 3.7 20.5 1.0
MG A:MG802 3.8 32.8 1.0
CG A:HIS563 4.1 22.4 1.0
ND1 A:HIS563 4.2 23.9 1.0
CD2 A:HIS525 4.3 25.2 1.0
CG A:HIS529 4.3 22.0 1.0
ND1 A:HIS529 4.3 23.3 1.0
CB A:ASP564 4.4 21.6 1.0
CB A:ASP674 4.4 24.8 1.0
O A:HOH930 4.4 32.3 1.0
NE2 A:HIS525 4.5 24.2 1.0
CG2 A:VAL533 4.7 18.7 1.0
O A:ASP674 4.8 23.7 1.0
CA A:ASP674 4.8 24.1 1.0

Zinc binding site 2 out of 4 in 5sgi

Go back to Zinc Binding Sites List in 5sgi
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:26.8
occ:1.00
 NE2 B:HIS563 2.1 19.1 1.0
OD2 B:ASP564 2.2 18.7 1.0
OD1 B:ASP674 2.2 16.7 1.0
NE2 B:HIS529 2.3 19.9 1.0
CD2 B:HIS563 3.0 18.7 1.0
CG B:ASP674 3.1 20.3 1.0
CG B:ASP564 3.1 19.6 1.0
CD2 B:HIS529 3.2 21.8 1.0
CE1 B:HIS563 3.2 19.9 1.0
OD2 B:ASP674 3.2 19.6 1.0
CE1 B:HIS529 3.3 22.4 1.0
OD1 B:ASP564 3.6 19.8 1.0
MG B:MG802 3.6 26.9 1.0
CD2 B:HIS525 4.1 20.3 1.0
CG B:HIS563 4.2 19.6 1.0
ND1 B:HIS563 4.2 19.5 1.0
CB B:ASP564 4.3 17.5 1.0
O B:HOH970 4.3 35.3 1.0
CG B:HIS529 4.4 21.5 1.0
NE2 B:HIS525 4.4 23.8 1.0
ND1 B:HIS529 4.4 20.3 1.0
CB B:ASP674 4.5 21.0 1.0
CG2 B:VAL533 4.8 18.6 1.0
CA B:ASP674 4.9 21.3 1.0
O B:ASP674 5.0 20.9 1.0

Zinc binding site 3 out of 4 in 5sgi

Go back to Zinc Binding Sites List in 5sgi
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:29.2
occ:1.00
 NE2 C:HIS529 2.1 20.0 1.0
OD2 C:ASP564 2.1 18.8 1.0
OD1 C:ASP674 2.2 18.6 1.0
NE2 C:HIS563 2.2 25.0 1.0
CD2 C:HIS563 3.0 19.5 1.0
CD2 C:HIS529 3.0 23.4 1.0
CG C:ASP674 3.1 23.0 1.0
CG C:ASP564 3.1 20.2 1.0
CE1 C:HIS529 3.1 21.1 1.0
CE1 C:HIS563 3.3 23.9 1.0
OD2 C:ASP674 3.4 29.6 1.0
OD1 C:ASP564 3.6 19.8 1.0
MG C:MG802 3.8 34.8 1.0
CD2 C:HIS525 4.1 23.4 1.0
CG C:HIS529 4.2 22.7 1.0
CG C:HIS563 4.2 23.2 1.0
ND1 C:HIS529 4.2 22.8 1.0
ND1 C:HIS563 4.3 22.8 1.0
CB C:ASP564 4.4 18.4 1.0
O C:HOH1009 4.4 27.9 1.0
NE2 C:HIS525 4.4 20.6 1.0
CB C:ASP674 4.5 23.4 1.0
O C:HOH1072 4.7 59.3 1.0
CG2 C:VAL533 4.8 20.1 1.0
CA C:ASP674 4.8 23.1 1.0

Zinc binding site 4 out of 4 in 5sgi

Go back to Zinc Binding Sites List in 5sgi
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine


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-(3- Methylphenoxy)-2-(4-Pyridin-2-Ylpiperazin-1-Yl)-9H-Purine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.7
occ:1.00
 NE2 D:HIS529 2.2 29.4 1.0
OD2 D:ASP564 2.2 26.1 1.0
NE2 D:HIS563 2.2 21.5 1.0
OD1 D:ASP674 2.3 25.2 1.0
CD2 D:HIS563 3.0 22.1 1.0
CG D:ASP564 3.1 27.7 1.0
CG D:ASP674 3.1 26.7 1.0
CD2 D:HIS529 3.1 26.8 1.0
CE1 D:HIS529 3.2 26.6 1.0
OD2 D:ASP674 3.3 26.9 1.0
CE1 D:HIS563 3.4 24.6 1.0
OD1 D:ASP564 3.6 27.9 1.0
MG D:MG802 3.9 46.3 1.0
CD2 D:HIS525 4.1 26.5 1.0
O D:HOH942 4.2 39.5 1.0
CG D:HIS563 4.2 24.1 1.0
CG D:HIS529 4.3 25.3 1.0
CB D:ASP564 4.3 27.1 1.0
ND1 D:HIS529 4.3 24.0 1.0
NE2 D:HIS525 4.4 30.0 1.0
ND1 D:HIS563 4.4 23.9 1.0
CB D:ASP674 4.5 25.1 1.0
CG2 D:VAL533 4.7 25.5 1.0
O D:ASP674 4.8 30.2 1.0
CA D:ASP674 4.9 24.0 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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