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Zinc in PDB 5si7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione, PDB code: 5si7 was solved by C.Joseph, J.Benz, A.Flohr, M.Boehringer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.50 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.21, 135.21, 235.625, 90, 90, 120
R / Rfree (%) 19.1 / 23.3

Other elements in 5si7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione 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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione (pdb code 5si7). 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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione, PDB code: 5si7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si7

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:30.1
occ:1.00
 OD2 A:ASP564 2.1 25.3 1.0
NE2 A:HIS529 2.1 25.7 1.0
NE2 A:HIS563 2.2 24.5 1.0
OD1 A:ASP674 2.2 28.0 1.0
O A:HOH992 2.2 39.8 1.0
O A:HOH984 2.3 27.0 1.0
CD2 A:HIS529 3.0 24.2 1.0
CD2 A:HIS563 3.0 23.5 1.0
CG A:ASP674 3.1 27.4 1.0
CG A:ASP564 3.1 24.5 1.0
CE1 A:HIS563 3.2 24.8 1.0
CE1 A:HIS529 3.2 24.7 1.0
OD2 A:ASP674 3.3 32.1 1.0
OD1 A:ASP564 3.6 23.5 1.0
MG A:MG802 3.8 24.5 1.0
CD2 A:HIS525 4.1 27.3 1.0
CG A:HIS563 4.2 24.2 1.0
CG A:HIS529 4.2 23.6 1.0
ND1 A:HIS563 4.2 24.1 1.0
O A:HOH968 4.3 26.1 1.0
ND1 A:HIS529 4.3 23.6 1.0
CB A:ASP564 4.3 25.7 1.0
O A:HOH1007 4.3 20.5 1.0
NE2 A:HIS525 4.4 26.0 1.0
CB A:ASP674 4.5 25.4 1.0
O A:HOH957 4.6 19.0 1.0
CG2 A:VAL533 4.7 22.7 1.0
O A:ASP674 4.8 25.5 1.0
CA A:ASP674 4.9 25.3 1.0
O A:HOH1020 4.9 44.1 1.0

Zinc binding site 2 out of 4 in 5si7

Go back to Zinc Binding Sites List in 5si7
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:28.7
occ:1.00
 OD2 B:ASP564 2.1 25.3 1.0
OD1 B:ASP674 2.2 22.7 1.0
NE2 B:HIS563 2.2 21.6 1.0
NE2 B:HIS529 2.2 22.8 1.0
O B:HOH968 2.2 19.5 1.0
O B:HOH987 2.3 33.6 1.0
CD2 B:HIS529 3.1 22.2 1.0
CD2 B:HIS563 3.1 22.1 1.0
CG B:ASP674 3.1 22.7 1.0
CG B:ASP564 3.1 24.2 1.0
CE1 B:HIS563 3.2 21.1 1.0
CE1 B:HIS529 3.2 24.1 1.0
OD2 B:ASP674 3.4 25.1 1.0
OD1 B:ASP564 3.6 23.6 1.0
MG B:MG802 3.8 20.8 1.0
O B:HOH1007 4.0 19.9 1.0
CD2 B:HIS525 4.1 22.7 1.0
O B:HOH964 4.1 28.1 1.0
CG B:HIS563 4.2 22.8 1.0
ND1 B:HIS563 4.3 22.0 1.0
CG B:HIS529 4.3 22.0 1.0
ND1 B:HIS529 4.3 21.5 1.0
CB B:ASP564 4.3 24.5 1.0
CB B:ASP674 4.4 22.6 1.0
NE2 B:HIS525 4.5 22.9 1.0
O B:HOH959 4.6 21.2 1.0
CG2 B:VAL533 4.7 23.0 1.0
O B:ASP674 4.8 25.0 1.0
CA B:ASP674 4.8 23.0 1.0

Zinc binding site 3 out of 4 in 5si7

Go back to Zinc Binding Sites List in 5si7
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:30.8
occ:1.00
 OD2 C:ASP564 2.1 26.1 1.0
NE2 C:HIS529 2.1 23.8 1.0
OD1 C:ASP674 2.1 23.8 1.0
O C:HOH936 2.2 24.1 1.0
NE2 C:HIS563 2.2 26.3 1.0
O C:HOH961 2.3 43.1 1.0
CD2 C:HIS563 3.0 25.5 1.0
CG C:ASP674 3.0 26.3 1.0
CD2 C:HIS529 3.0 25.7 1.0
CG C:ASP564 3.1 24.7 1.0
CE1 C:HIS529 3.2 24.2 1.0
OD2 C:ASP674 3.3 29.5 1.0
CE1 C:HIS563 3.3 27.5 1.0
OD1 C:ASP564 3.7 24.7 1.0
MG C:MG802 3.8 27.1 1.0
CD2 C:HIS525 4.0 28.0 1.0
CG C:HIS563 4.2 25.1 1.0
CG C:HIS529 4.2 26.3 1.0
O C:HOH1012 4.2 23.4 1.0
ND1 C:HIS529 4.3 24.1 1.0
O C:HOH959 4.3 37.5 1.0
CB C:ASP564 4.3 24.3 1.0
ND1 C:HIS563 4.3 25.4 1.0
CB C:ASP674 4.4 26.6 1.0
NE2 C:HIS525 4.4 28.4 1.0
O C:HOH950 4.6 23.1 1.0
CG2 C:VAL533 4.7 23.0 1.0
CA C:ASP674 4.8 27.4 1.0
O C:ASP674 4.8 28.4 1.0
O C:HOH1005 4.8 44.7 1.0

Zinc binding site 4 out of 4 in 5si7

Go back to Zinc Binding Sites List in 5si7
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione


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 2- Benzyl-6,6-Dimethyl-1H-Imidazo[4,5-H]Isoquinoline-7,9-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:36.2
occ:1.00
 O D:HOH926 2.0 25.5 1.0
NE2 D:HIS563 2.1 25.3 1.0
OD2 D:ASP564 2.2 34.8 1.0
NE2 D:HIS529 2.2 33.4 1.0
OD1 D:ASP674 2.3 32.3 1.0
O D:HOH974 2.4 36.0 1.0
CD2 D:HIS563 3.0 27.1 1.0
CG D:ASP674 3.1 32.5 1.0
CG D:ASP564 3.1 32.2 1.0
CD2 D:HIS529 3.1 35.4 1.0
CE1 D:HIS563 3.2 27.9 1.0
CE1 D:HIS529 3.3 37.0 1.0
OD2 D:ASP674 3.3 31.9 1.0
OD1 D:ASP564 3.6 33.1 1.0
MG D:MG802 3.9 35.6 1.0
O D:HOH959 4.1 35.2 1.0
O D:HOH942 4.2 33.4 1.0
CG D:HIS563 4.2 26.9 1.0
CD2 D:HIS525 4.2 33.0 1.0
CB D:ASP564 4.3 31.0 1.0
ND1 D:HIS563 4.3 26.2 1.0
CG D:HIS529 4.3 35.0 1.0
ND1 D:HIS529 4.4 35.3 1.0
O D:HOH924 4.5 26.4 1.0
CB D:ASP674 4.5 33.0 1.0
NE2 D:HIS525 4.7 35.7 1.0
CG2 D:VAL533 4.7 34.0 1.0
O D:ASP674 4.8 34.8 1.0
CA D:ASP674 4.9 32.2 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 05:41:13 2024

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