Zinc in PDB 5sh0: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide, PDB code: 5sh0 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) 43.58 / 2.29
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.07, 135.07, 234.801, 90, 90, 120
R / Rfree (%) 17.9 / 22.3

Other elements in 5sh0:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide 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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide (pdb code 5sh0). 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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide, PDB code: 5sh0:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sh0

Go back to Zinc Binding Sites List in 5sh0
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:41.6
occ:1.00
 OD2 A:ASP564 2.1 33.0 1.0
O A:HOH939 2.1 33.5 1.0
NE2 A:HIS563 2.1 30.0 1.0
NE2 A:HIS529 2.1 37.0 1.0
OD1 A:ASP674 2.2 44.6 1.0
O A:HOH925 2.7 44.8 1.0
CD2 A:HIS563 3.0 31.4 1.0
CG A:ASP674 3.0 38.8 1.0
CD2 A:HIS529 3.1 35.1 1.0
CE1 A:HIS529 3.1 34.9 1.0
CG A:ASP564 3.1 33.0 1.0
CE1 A:HIS563 3.2 34.6 1.0
OD2 A:ASP674 3.3 44.3 1.0
MG A:MG802 3.7 31.8 1.0
OD1 A:ASP564 3.7 31.4 1.0
O A:HOH976 4.0 33.0 1.0
O A:HOH952 4.1 43.0 1.0
CD2 A:HIS525 4.2 36.4 1.0
CG A:HIS563 4.2 30.7 1.0
ND1 A:HIS529 4.2 34.7 1.0
CG A:HIS529 4.2 33.3 1.0
ND1 A:HIS563 4.2 31.5 1.0
CB A:ASP564 4.3 30.4 1.0
CB A:ASP674 4.4 36.9 1.0
NE2 A:HIS525 4.5 37.1 1.0
O A:HOH906 4.5 27.9 1.0
O A:ASP674 4.8 36.7 1.0
CG2 A:VAL533 4.8 29.6 1.0
CA A:ASP674 4.9 34.1 1.0
O A:HOH949 4.9 32.0 1.0

Zinc binding site 2 out of 4 in 5sh0

Go back to Zinc Binding Sites List in 5sh0
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:37.3
occ:1.00
 OD2 B:ASP564 2.1 36.5 1.0
O B:HOH959 2.1 24.8 1.0
NE2 B:HIS563 2.2 32.3 1.0
NE2 B:HIS529 2.2 30.2 1.0
OD1 B:ASP674 2.2 33.4 1.0
O B:HOH916 2.8 43.3 1.0
CD2 B:HIS563 3.0 32.9 1.0
CG B:ASP564 3.1 33.2 1.0
CE1 B:HIS529 3.1 30.2 1.0
CG B:ASP674 3.1 33.3 1.0
CD2 B:HIS529 3.2 31.9 1.0
CE1 B:HIS563 3.2 33.0 1.0
OD2 B:ASP674 3.4 38.7 1.0
OD1 B:ASP564 3.6 33.9 1.0
MG B:MG802 3.7 29.8 1.0
O B:HOH973 4.0 23.9 1.0
CD2 B:HIS525 4.1 35.7 1.0
O B:HOH961 4.2 42.1 1.0
CG B:HIS563 4.2 31.6 1.0
ND1 B:HIS529 4.3 28.6 1.0
ND1 B:HIS563 4.3 31.7 1.0
CG B:HIS529 4.3 28.9 1.0
CB B:ASP564 4.3 31.9 1.0
CB B:ASP674 4.5 33.9 1.0
NE2 B:HIS525 4.5 33.5 1.0
O B:HOH944 4.6 32.0 1.0
O B:ASP674 4.8 30.3 1.0
CG2 B:VAL533 4.8 28.6 1.0
CA B:ASP674 4.9 32.3 1.0

Zinc binding site 3 out of 4 in 5sh0

Go back to Zinc Binding Sites List in 5sh0
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:40.7
occ:1.00
 O C:HOH924 1.9 29.6 1.0
OD2 C:ASP564 2.1 34.3 1.0
NE2 C:HIS529 2.2 34.4 1.0
NE2 C:HIS563 2.2 35.4 1.0
OD1 C:ASP674 2.2 34.3 1.0
O C:HOH909 2.8 52.1 1.0
CG C:ASP674 3.0 31.2 1.0
CD2 C:HIS563 3.0 32.6 1.0
CG C:ASP564 3.1 32.9 1.0
OD2 C:ASP674 3.1 32.1 1.0
CD2 C:HIS529 3.2 35.6 1.0
CE1 C:HIS529 3.2 35.8 1.0
CE1 C:HIS563 3.3 34.8 1.0
OD1 C:ASP564 3.6 34.6 1.0
MG C:MG802 3.7 32.1 1.0
O C:HOH977 4.1 30.2 1.0
O C:HOH958 4.1 41.7 1.0
CD2 C:HIS525 4.2 39.0 1.0
CG C:HIS563 4.2 32.1 1.0
ND1 C:HIS529 4.3 34.6 1.0
CG C:HIS529 4.3 32.1 1.0
CB C:ASP564 4.3 30.9 1.0
ND1 C:HIS563 4.3 31.4 1.0
CB C:ASP674 4.4 33.2 1.0
NE2 C:HIS525 4.5 39.9 1.0
O C:HOH940 4.5 32.6 1.0
O C:ASP674 4.8 38.0 1.0
CG2 C:VAL533 4.8 33.4 1.0
CA C:ASP674 4.8 36.1 1.0

Zinc binding site 4 out of 4 in 5sh0

Go back to Zinc Binding Sites List in 5sh0
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide


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 N-(1, 3-Dimethyl-2-Oxobenzimidazol-5-Yl)-2-[Methylsulfonyl(Naphthalen-1- Yl)Amino]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:48.7
occ:1.00
 O D:HOH920 1.9 32.8 1.0
NE2 D:HIS563 2.1 35.1 1.0
OD2 D:ASP564 2.2 46.0 1.0
OD1 D:ASP674 2.3 43.3 1.0
NE2 D:HIS529 2.3 44.6 1.0
O D:HOH927 2.6 43.2 1.0
CD2 D:HIS563 3.0 36.4 1.0
CG D:ASP674 3.1 40.6 1.0
CG D:ASP564 3.1 39.7 1.0
CD2 D:HIS529 3.2 47.6 1.0
CE1 D:HIS563 3.2 41.0 1.0
OD2 D:ASP674 3.3 45.6 1.0
CE1 D:HIS529 3.3 45.7 1.0
OD1 D:ASP564 3.7 40.7 1.0
MG D:MG802 3.8 45.7 1.0
O D:HOH928 3.9 36.6 1.0
CD2 D:HIS525 4.2 55.6 1.0
CG D:HIS563 4.2 35.9 1.0
CB D:ASP564 4.2 41.1 1.0
ND1 D:HIS563 4.3 37.3 1.0
CG D:HIS529 4.4 43.9 1.0
ND1 D:HIS529 4.4 45.4 1.0
CB D:ASP674 4.5 44.5 1.0
O D:HOH912 4.5 36.9 1.0
NE2 D:HIS525 4.6 52.8 1.0
O D:ASP674 4.8 50.8 1.0
CG2 D:VAL533 4.9 45.6 1.0
CA D:ASP674 4.9 44.9 1.0
O D:HOH906 5.0 38.1 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 05:22:59 2024

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