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Zinc in PDB 5sjw: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjw was solved by C.Joseph, J.Benz, A.Flohr, J.Peters, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.67 / 1.95
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.122, 135.122, 235.325, 90, 90, 120
R / Rfree (%) 17.3 / 20.7

Other elements in 5sjw:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Chlorine (Cl) 5 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide (pdb code 5sjw). 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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide, PDB code: 5sjw:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjw

Go back to Zinc Binding Sites List in 5sjw
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide


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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:25.3
occ:1.00
 NE2 A:HIS563 2.1 20.1 1.0
O A:HOH933 2.1 21.7 1.0
OD2 A:ASP564 2.1 19.8 1.0
OD1 A:ASP674 2.1 22.9 1.0
NE2 A:HIS529 2.2 22.2 1.0
O A:HOH1036 2.2 27.5 1.0
CD2 A:HIS563 3.0 19.4 1.0
CG A:ASP674 3.0 23.7 1.0
CG A:ASP564 3.1 19.8 1.0
CD2 A:HIS529 3.1 21.7 1.0
CE1 A:HIS529 3.2 22.2 1.0
CE1 A:HIS563 3.2 20.8 1.0
OD2 A:ASP674 3.3 29.0 1.0
OD1 A:ASP564 3.6 18.8 1.0
MG A:MG802 3.8 20.7 1.0
O A:HOH1059 4.1 21.6 1.0
CD2 A:HIS525 4.1 24.9 1.0
CG A:HIS563 4.2 19.7 1.0
ND1 A:HIS563 4.2 19.9 1.0
O A:HOH958 4.3 27.6 1.0
ND1 A:HIS529 4.3 20.8 1.0
CG A:HIS529 4.3 21.4 1.0
CB A:ASP564 4.3 19.6 1.0
CB A:ASP674 4.4 22.7 1.0
NE2 A:HIS525 4.5 25.2 1.0
O A:HOH943 4.6 17.2 1.0
O A:HOH1089 4.7 52.6 1.0
CG2 A:VAL533 4.7 19.0 1.0
O A:ASP674 4.8 22.4 1.0
CA A:ASP674 4.8 22.4 1.0

Zinc binding site 2 out of 4 in 5sjw

Go back to Zinc Binding Sites List in 5sjw
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide


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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:23.8
occ:1.00
 O B:HOH917 2.1 15.8 1.0
NE2 B:HIS563 2.1 17.9 1.0
NE2 B:HIS529 2.1 19.6 1.0
OD1 B:ASP674 2.1 20.2 1.0
OD2 B:ASP564 2.2 18.2 1.0
O B:HOH1030 2.2 26.8 1.0
CG B:ASP674 3.0 22.6 1.0
CD2 B:HIS563 3.0 18.8 1.0
CE1 B:HIS529 3.1 20.3 1.0
CG B:ASP564 3.1 19.6 1.0
CD2 B:HIS529 3.1 19.8 1.0
CE1 B:HIS563 3.1 19.6 1.0
OD2 B:ASP674 3.2 22.8 1.0
OD1 B:ASP564 3.6 18.9 1.0
MG B:MG802 3.8 16.4 1.0
O B:HOH1062 4.0 20.6 1.0
O B:HOH997 4.0 27.2 1.0
CD2 B:HIS525 4.1 22.9 1.0
CG B:HIS563 4.2 19.1 1.0
ND1 B:HIS529 4.2 19.8 1.0
ND1 B:HIS563 4.2 19.7 1.0
CG B:HIS529 4.3 19.8 1.0
CB B:ASP564 4.3 18.8 1.0
NE2 B:HIS525 4.3 23.1 1.0
CB B:ASP674 4.4 21.0 1.0
O B:HOH1076 4.5 47.2 1.0
O B:HOH991 4.7 16.3 1.0
CG2 B:VAL533 4.7 20.0 1.0
CA B:ASP674 4.8 20.8 1.0
O B:ASP674 4.9 20.6 1.0

Zinc binding site 3 out of 4 in 5sjw

Go back to Zinc Binding Sites List in 5sjw
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide


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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:26.5
occ:1.00
 O C:HOH940 2.1 19.4 1.0
OD2 C:ASP564 2.1 20.5 1.0
NE2 C:HIS529 2.1 21.4 1.0
OD1 C:ASP674 2.1 21.1 1.0
NE2 C:HIS563 2.2 19.3 1.0
O C:HOH1009 2.3 27.6 1.0
CG C:ASP674 3.0 24.4 1.0
CD2 C:HIS563 3.0 19.5 1.0
CD2 C:HIS529 3.1 21.1 1.0
CG C:ASP564 3.1 21.2 1.0
CE1 C:HIS529 3.2 21.9 1.0
CE1 C:HIS563 3.2 18.9 1.0
OD2 C:ASP674 3.3 29.2 1.0
OD1 C:ASP564 3.6 21.1 1.0
MG C:MG802 3.8 22.5 1.0
O C:HOH1048 4.0 22.1 1.0
CD2 C:HIS525 4.1 26.3 1.0
O C:HOH981 4.1 31.2 1.0
CG C:HIS563 4.2 19.4 1.0
CG C:HIS529 4.2 21.7 1.0
ND1 C:HIS529 4.3 21.9 1.0
ND1 C:HIS563 4.3 19.6 1.0
CB C:ASP564 4.3 19.4 1.0
CB C:ASP674 4.4 24.9 1.0
NE2 C:HIS525 4.4 26.2 1.0
O C:HOH1079 4.5 46.9 1.0
O C:HOH985 4.7 21.9 1.0
CG2 C:VAL533 4.7 22.2 1.0
CA C:ASP674 4.8 23.9 1.0
O C:ASP674 4.9 24.1 1.0

Zinc binding site 4 out of 4 in 5sjw

Go back to Zinc Binding Sites List in 5sjw
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide


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 4- Chloro-2-(2-Methylpropyl)-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole- 3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.2
occ:1.00
 O D:HOH924 2.0 21.4 1.0
NE2 D:HIS563 2.1 23.7 1.0
NE2 D:HIS529 2.1 32.1 1.0
OD2 D:ASP564 2.2 28.4 1.0
OD1 D:ASP674 2.2 26.9 1.0
O D:HOH959 2.3 33.8 1.0
CD2 D:HIS563 3.0 25.1 1.0
CG D:ASP674 3.1 31.1 1.0
CD2 D:HIS529 3.1 33.0 1.0
CG D:ASP564 3.1 27.0 1.0
CE1 D:HIS529 3.2 32.8 1.0
CE1 D:HIS563 3.2 24.7 1.0
OD2 D:ASP674 3.3 31.5 1.0
OD1 D:ASP564 3.6 28.4 1.0
MG D:MG802 3.8 30.3 1.0
O D:HOH1033 4.0 28.4 1.0
O D:HOH978 4.1 36.4 1.0
CD2 D:HIS525 4.1 33.1 1.0
CG D:HIS563 4.2 23.6 1.0
ND1 D:HIS563 4.3 23.0 1.0
ND1 D:HIS529 4.3 29.1 1.0
CG D:HIS529 4.3 30.9 1.0
CB D:ASP564 4.3 26.6 1.0
NE2 D:HIS525 4.4 34.0 1.0
CB D:ASP674 4.5 27.9 1.0
O D:HOH929 4.7 29.5 1.0
CG2 D:VAL533 4.7 29.0 1.0
O D:ASP674 4.8 29.9 1.0
CA D:ASP674 4.9 28.6 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 06:08:27 2024

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