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Zinc in PDB 5sii: Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine, PDB code: 5sii was solved by C.Joseph, J.Benz, A.Flohr, P.Zeller, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.71 / 2.18
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.531, 135.531, 235.479, 90, 90, 120
R / Rfree (%) 17.5 / 22.5

Other elements in 5sii:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine 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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine (pdb code 5sii). 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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine, PDB code: 5sii:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sii

Go back to Zinc Binding Sites List in 5sii
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:36.6
occ:1.00
 NE2 A:HIS563 2.0 31.5 1.0
OD2 A:ASP564 2.1 31.0 1.0
NE2 A:HIS529 2.1 38.2 1.0
O A:HOH971 2.2 30.7 1.0
OD1 A:ASP674 2.2 39.6 1.0
O A:HOH967 2.2 39.2 1.0
CD2 A:HIS563 3.0 28.3 1.0
CE1 A:HIS563 3.1 32.0 1.0
CD2 A:HIS529 3.1 37.2 1.0
CG A:ASP674 3.1 39.0 1.0
CG A:ASP564 3.1 31.5 1.0
CE1 A:HIS529 3.2 33.8 1.0
OD2 A:ASP674 3.3 40.5 1.0
OD1 A:ASP564 3.6 34.5 1.0
MG A:MG802 3.7 31.6 1.0
O A:HOH987 4.1 28.9 1.0
CG A:HIS563 4.1 32.7 1.0
ND1 A:HIS563 4.1 30.4 1.0
CD2 A:HIS525 4.2 37.6 1.0
O A:HOH974 4.2 50.6 1.0
CG A:HIS529 4.2 30.8 1.0
ND1 A:HIS529 4.2 34.0 1.0
CB A:ASP564 4.3 29.9 1.0
NE2 A:HIS525 4.5 38.7 1.0
CB A:ASP674 4.5 34.3 1.0
O A:HOH908 4.6 27.6 1.0
CG2 A:VAL533 4.7 32.0 1.0
O A:ASP674 4.9 34.9 1.0
CA A:ASP674 4.9 32.0 1.0

Zinc binding site 2 out of 4 in 5sii

Go back to Zinc Binding Sites List in 5sii
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.9
occ:1.00
 NE2 B:HIS563 2.1 28.4 1.0
OD1 B:ASP674 2.1 30.5 1.0
OD2 B:ASP564 2.2 30.5 1.0
NE2 B:HIS529 2.2 27.4 1.0
O B:HOH957 2.2 25.2 1.0
O B:HOH980 2.4 38.5 1.0
CD2 B:HIS563 3.0 31.9 1.0
CG B:ASP674 3.0 31.8 1.0
CD2 B:HIS529 3.1 33.2 1.0
CG B:ASP564 3.1 28.8 1.0
CE1 B:HIS563 3.2 33.1 1.0
CE1 B:HIS529 3.2 28.8 1.0
OD2 B:ASP674 3.3 39.2 1.0
OD1 B:ASP564 3.6 29.9 1.0
MG B:MG802 3.7 30.9 1.0
O B:HOH996 3.9 26.9 1.0
CD2 B:HIS525 4.1 34.2 1.0
CG B:HIS563 4.2 29.9 1.0
ND1 B:HIS563 4.2 28.7 1.0
CG B:HIS529 4.3 29.9 1.0
ND1 B:HIS529 4.3 28.7 1.0
CB B:ASP564 4.3 27.9 1.0
O B:HOH973 4.4 54.7 1.0
CB B:ASP674 4.4 32.7 1.0
NE2 B:HIS525 4.4 36.6 1.0
O B:HOH943 4.6 25.0 1.0
CG2 B:VAL533 4.8 27.0 1.0
CA B:ASP674 4.8 29.1 1.0
O B:ASP674 4.9 29.9 1.0

Zinc binding site 3 out of 4 in 5sii

Go back to Zinc Binding Sites List in 5sii
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.9
occ:1.00
 O C:HOH948 2.0 24.3 1.0
NE2 C:HIS529 2.1 35.6 1.0
OD1 C:ASP674 2.1 29.7 1.0
NE2 C:HIS563 2.2 32.1 1.0
OD2 C:ASP564 2.2 30.5 1.0
O C:HOH965 2.2 42.2 1.0
CD2 C:HIS529 3.0 33.0 1.0
CG C:ASP674 3.0 32.2 1.0
CD2 C:HIS563 3.0 31.5 1.0
CE1 C:HIS529 3.2 35.6 1.0
CG C:ASP564 3.2 30.4 1.0
CE1 C:HIS563 3.2 30.8 1.0
OD2 C:ASP674 3.3 38.7 1.0
OD1 C:ASP564 3.7 29.3 1.0
MG C:MG802 3.8 28.3 1.0
O C:HOH1000 4.1 50.0 1.0
CD2 C:HIS525 4.1 36.3 1.0
O C:HOH995 4.2 31.3 1.0
CG C:HIS529 4.2 29.8 1.0
CG C:HIS563 4.2 30.4 1.0
ND1 C:HIS529 4.2 30.7 1.0
ND1 C:HIS563 4.3 30.0 1.0
NE2 C:HIS525 4.3 36.4 1.0
CB C:ASP564 4.3 28.5 1.0
CB C:ASP674 4.4 33.5 1.0
O C:HOH914 4.5 28.9 1.0
CG2 C:VAL533 4.8 34.0 1.0
CA C:ASP674 4.8 33.5 1.0
O C:ASP674 4.9 32.7 1.0

Zinc binding site 4 out of 4 in 5sii

Go back to Zinc Binding Sites List in 5sii
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 1-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine


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-(3, 4-Dimethoxyphenyl)-5-Ethyl-7,8-Dimethoxy-4-Methyl-5H-2,3- Benzodiazepine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:42.3
occ:1.00
 O D:HOH945 2.1 28.9 1.0
NE2 D:HIS563 2.1 31.2 1.0
OD1 D:ASP674 2.2 47.1 1.0
NE2 D:HIS529 2.2 40.0 1.0
OD2 D:ASP564 2.2 36.0 1.0
O D:HOH941 2.3 43.1 1.0
CD2 D:HIS563 3.0 33.2 1.0
CG D:ASP674 3.0 42.8 1.0
CD2 D:HIS529 3.1 42.9 1.0
CG D:ASP564 3.2 37.9 1.0
CE1 D:HIS529 3.2 42.1 1.0
CE1 D:HIS563 3.3 35.5 1.0
OD2 D:ASP674 3.3 49.9 1.0
OD1 D:ASP564 3.7 38.7 1.0
MG D:MG802 3.8 38.0 1.0
CD2 D:HIS525 4.1 42.5 1.0
O D:HOH957 4.1 40.0 1.0
CG D:HIS563 4.2 33.8 1.0
CB D:ASP564 4.3 33.8 1.0
CG D:HIS529 4.3 34.8 1.0
ND1 D:HIS563 4.3 34.7 1.0
ND1 D:HIS529 4.3 40.6 1.0
NE2 D:HIS525 4.4 47.5 1.0
CB D:ASP674 4.4 42.9 1.0
O D:HOH913 4.5 30.2 1.0
CG2 D:VAL533 4.8 37.8 1.0
CA D:ASP674 4.8 39.4 1.0
O D:ASP674 4.9 50.0 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 05:45:11 2024

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