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Zinc in PDB 5seo: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione, PDB code: 5seo was solved by C.Joseph, J.Benz, D.Schlatter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.52 / 2.10
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.277, 135.277, 235.581, 90, 90, 120
R / Rfree (%) 18.3 / 22.8

Other elements in 5seo:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione (pdb code 5seo). 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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione, PDB code: 5seo:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5seo

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:34.2
occ:1.00
 NE2 A:HIS563 2.0 26.0 1.0
OD2 A:ASP564 2.1 32.2 1.0
O A:HOH945 2.1 30.4 1.0
NE2 A:HIS529 2.2 31.2 1.0
OD1 A:ASP674 2.2 34.0 1.0
O A:HOH986 2.4 39.2 1.0
CD2 A:HIS563 3.0 26.7 1.0
CG A:ASP674 3.1 37.0 1.0
CG A:ASP564 3.1 30.2 1.0
CD2 A:HIS529 3.1 32.1 1.0
CE1 A:HIS563 3.1 29.6 1.0
CE1 A:HIS529 3.2 29.3 1.0
OD2 A:ASP674 3.3 40.4 1.0
OD1 A:ASP564 3.6 27.1 1.0
MG A:MG802 3.8 28.4 1.0
O A:HOH953 4.1 37.4 1.0
O A:HOH1002 4.1 26.1 1.0
CG A:HIS563 4.1 26.9 1.0
ND1 A:HIS563 4.2 26.1 1.0
CD2 A:HIS525 4.2 36.1 1.0
CG A:HIS529 4.3 31.3 1.0
CB A:ASP564 4.3 27.0 1.0
ND1 A:HIS529 4.3 29.7 1.0
CB A:ASP674 4.5 34.1 1.0
NE2 A:HIS525 4.6 35.4 1.0
O A:HOH927 4.6 26.3 1.0
CG2 A:VAL533 4.7 26.9 1.0
O A:ASP674 4.8 32.8 1.0
CA A:ASP674 4.9 29.6 1.0

Zinc binding site 2 out of 4 in 5seo

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:33.8
occ:1.00
 O B:HOH925 2.1 25.2 1.0
NE2 B:HIS563 2.1 27.0 1.0
OD2 B:ASP564 2.1 29.6 1.0
OD1 B:ASP674 2.2 28.1 1.0
NE2 B:HIS529 2.2 28.5 1.0
O B:HOH995 2.3 40.7 1.0
CG B:ASP674 3.0 30.8 1.0
CD2 B:HIS563 3.0 28.1 1.0
CD2 B:HIS529 3.1 28.2 1.0
CG B:ASP564 3.1 30.8 1.0
CE1 B:HIS563 3.2 28.8 1.0
OD2 B:ASP674 3.2 32.4 1.0
CE1 B:HIS529 3.2 30.6 1.0
OD1 B:ASP564 3.6 28.4 1.0
MG B:MG802 3.8 26.4 1.0
O B:HOH1000 4.1 26.2 1.0
CD2 B:HIS525 4.1 32.5 1.0
O B:HOH990 4.2 37.1 1.0
CG B:HIS563 4.2 27.7 1.0
CG B:HIS529 4.2 30.5 1.0
ND1 B:HIS563 4.3 26.5 1.0
ND1 B:HIS529 4.3 30.1 1.0
CB B:ASP564 4.3 26.5 1.0
CB B:ASP674 4.4 30.0 1.0
NE2 B:HIS525 4.4 31.8 1.0
O B:HOH924 4.6 23.9 1.0
CG2 B:VAL533 4.7 26.9 1.0
CA B:ASP674 4.8 28.5 1.0
O B:ASP674 4.9 29.9 1.0
O B:HOH1024 5.0 53.6 1.0

Zinc binding site 3 out of 4 in 5seo

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Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:36.0
occ:1.00
 O C:HOH943 2.0 28.9 1.0
NE2 C:HIS529 2.1 29.6 1.0
NE2 C:HIS563 2.1 29.3 1.0
OD2 C:ASP564 2.2 31.1 1.0
OD1 C:ASP674 2.2 28.6 1.0
O C:HOH964 2.3 37.0 1.0
CD2 C:HIS563 3.0 27.4 1.0
CG C:ASP674 3.0 33.0 1.0
CD2 C:HIS529 3.1 28.6 1.0
CE1 C:HIS529 3.2 30.9 1.0
CG C:ASP564 3.2 31.1 1.0
OD2 C:ASP674 3.2 36.5 1.0
CE1 C:HIS563 3.2 29.3 1.0
OD1 C:ASP564 3.6 27.8 1.0
MG C:MG802 3.8 31.9 1.0
CD2 C:HIS525 4.0 35.7 1.0
O C:HOH991 4.1 28.1 1.0
CG C:HIS563 4.2 28.6 1.0
CG C:HIS529 4.2 33.2 1.0
ND1 C:HIS529 4.2 29.2 1.0
ND1 C:HIS563 4.3 26.8 1.0
CB C:ASP564 4.3 28.4 1.0
O C:HOH983 4.3 45.5 1.0
NE2 C:HIS525 4.4 35.9 1.0
CB C:ASP674 4.4 33.2 1.0
O C:HOH931 4.6 32.8 1.0
CG2 C:VAL533 4.7 29.0 1.0
CA C:ASP674 4.8 32.4 1.0
O C:ASP674 4.8 35.8 1.0

Zinc binding site 4 out of 4 in 5seo

Go back to Zinc Binding Sites List in 5seo
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-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-[2- (5-Methyl-2-Phenyl-1H-Imidazol-4-Yl)Ethyl]Isoindole-1,3-Dione within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:44.9
occ:1.00
 NE2 D:HIS563 2.0 36.9 1.0
O D:HOH911 2.1 33.8 1.0
NE2 D:HIS529 2.2 42.2 1.0
OD1 D:ASP674 2.2 40.0 1.0
OD2 D:ASP564 2.2 43.2 1.0
O D:HOH946 2.3 46.3 1.0
CD2 D:HIS563 2.9 39.8 1.0
CG D:ASP674 3.0 42.9 1.0
CG D:ASP564 3.1 38.1 1.0
CD2 D:HIS529 3.1 48.7 1.0
CE1 D:HIS563 3.2 41.0 1.0
OD2 D:ASP674 3.2 43.0 1.0
CE1 D:HIS529 3.2 42.8 1.0
OD1 D:ASP564 3.5 39.2 1.0
MG D:MG802 3.9 41.4 1.0
CG D:HIS563 4.1 36.4 1.0
O D:HOH956 4.1 38.0 1.0
O D:HOH926 4.2 50.6 1.0
ND1 D:HIS563 4.2 36.6 1.0
CD2 D:HIS525 4.2 46.1 1.0
CB D:ASP564 4.2 39.0 1.0
ND1 D:HIS529 4.3 40.7 1.0
CG D:HIS529 4.3 40.8 1.0
CB D:ASP674 4.4 42.1 1.0
O D:HOH921 4.5 39.4 1.0
NE2 D:HIS525 4.6 53.0 1.0
CG2 D:VAL533 4.7 45.1 1.0
O D:ASP674 4.9 43.7 1.0
CA D:ASP674 4.9 39.6 1.0

Reference:

A.Tosstorff, M.G.Rudolph, J.C.Cole, M.Reutlinger, C.Kramer, H.Schaffhauser, A.Nilly, A.Flohr, B.Kuhn. A High Quality, Industrial Data Set For Binding Affinity Prediction: Performance Comparison in Different Early Drug Discovery Scenarios. J.Comput.Aided Mol.Des. V. 36 753 2022.
ISSN: ESSN 1573-4951
PubMed: 36153472
DOI: 10.1007/S10822-022-00478-X
Page generated: Mon Oct 28 04:44:23 2024

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