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

Resolution Low / High (Å) 41.56 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.42, 135.42, 235.47, 90, 90, 120
R / Rfree (%) 17.4 / 22.5

Other elements in 5sji:

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

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

Zinc Binding Sites:

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

Zinc binding site 1 out of 4 in 5sji

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-Methyl-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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:26.4
occ:1.00
 NE2 A:HIS563 2.0 21.9 1.0
NE2 A:HIS529 2.1 22.8 1.0
OD2 A:ASP564 2.2 20.8 1.0
O A:HOH994 2.2 33.2 1.0
O A:HOH984 2.2 22.7 1.0
OD1 A:ASP674 2.2 24.5 1.0
CD2 A:HIS563 2.9 20.4 1.0
CD2 A:HIS529 3.0 22.6 1.0
CE1 A:HIS563 3.1 25.9 1.0
CG A:ASP674 3.1 24.9 1.0
CG A:ASP564 3.1 22.8 1.0
CE1 A:HIS529 3.2 22.7 1.0
OD2 A:ASP674 3.4 26.1 1.0
OD1 A:ASP564 3.6 19.4 1.0
MG A:MG802 3.8 22.1 1.0
CG A:HIS563 4.1 22.4 1.0
ND1 A:HIS563 4.1 22.4 1.0
CD2 A:HIS525 4.2 22.4 1.0
CG A:HIS529 4.2 22.0 1.0
ND1 A:HIS529 4.3 19.7 1.0
O A:HOH1034 4.3 21.9 1.0
CB A:ASP564 4.3 21.2 1.0
O A:HOH953 4.3 25.9 1.0
CB A:ASP674 4.4 22.4 1.0
O A:HOH916 4.5 17.8 1.0
NE2 A:HIS525 4.5 24.6 1.0
CG2 A:VAL533 4.7 18.1 1.0
CA A:ASP674 4.9 21.8 1.0
O A:ASP674 4.9 21.2 1.0

Zinc binding site 2 out of 4 in 5sji

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-Methyl-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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.8
occ:1.00
 OD1 B:ASP674 2.1 16.5 1.0
O B:HOH945 2.1 15.6 1.0
NE2 B:HIS563 2.1 17.7 1.0
OD2 B:ASP564 2.2 20.5 1.0
NE2 B:HIS529 2.2 20.5 1.0
O B:HOH984 2.4 37.6 1.0
CG B:ASP674 3.0 20.5 1.0
CD2 B:HIS563 3.0 17.7 1.0
CG B:ASP564 3.1 19.8 1.0
OD2 B:ASP674 3.2 19.3 1.0
CD2 B:HIS529 3.2 21.5 1.0
CE1 B:HIS529 3.2 20.9 1.0
CE1 B:HIS563 3.2 19.2 1.0
OD1 B:ASP564 3.5 19.3 1.0
MG B:MG802 3.7 17.1 1.0
O B:HOH1041 4.0 18.4 1.0
CD2 B:HIS525 4.0 20.3 1.0
CG B:HIS563 4.2 18.3 1.0
O B:HOH979 4.2 27.3 1.0
ND1 B:HIS563 4.3 17.6 1.0
CB B:ASP564 4.3 16.6 1.0
ND1 B:HIS529 4.3 17.5 1.0
CG B:HIS529 4.3 19.5 1.0
NE2 B:HIS525 4.4 22.1 1.0
CB B:ASP674 4.4 18.7 1.0
O B:HOH969 4.5 17.2 1.0
O B:HOH1077 4.5 38.3 1.0
CG2 B:VAL533 4.8 18.0 1.0
CA B:ASP674 4.9 20.1 1.0
O B:ASP674 4.9 22.2 1.0
O B:HOH939 5.0 17.8 1.0

Zinc binding site 3 out of 4 in 5sji

Go back to Zinc Binding Sites List in 5sji
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-Methyl-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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:26.8
occ:1.00
 NE2 C:HIS529 2.0 24.0 1.0
OD2 C:ASP564 2.1 20.5 1.0
O C:HOH943 2.2 18.1 1.0
NE2 C:HIS563 2.2 23.1 1.0
OD1 C:ASP674 2.2 20.0 1.0
O C:HOH1011 2.5 44.3 1.0
CD2 C:HIS563 3.0 20.3 1.0
CD2 C:HIS529 3.0 24.8 1.0
CE1 C:HIS529 3.1 22.5 1.0
CG C:ASP674 3.1 23.7 1.0
CG C:ASP564 3.1 20.3 1.0
CE1 C:HIS563 3.3 21.6 1.0
OD2 C:ASP674 3.3 29.8 1.0
OD1 C:ASP564 3.6 18.5 1.0
MG C:MG802 3.8 22.1 1.0
O C:HOH1019 4.1 25.2 1.0
CD2 C:HIS525 4.1 24.1 1.0
ND1 C:HIS529 4.2 22.7 1.0
CG C:HIS529 4.2 21.4 1.0
CG C:HIS563 4.2 21.2 1.0
CB C:ASP564 4.3 18.7 1.0
ND1 C:HIS563 4.3 22.2 1.0
O C:HOH1023 4.4 28.5 1.0
NE2 C:HIS525 4.4 22.8 1.0
O C:HOH1065 4.5 45.5 1.0
CB C:ASP674 4.5 22.5 1.0
O C:HOH947 4.6 23.1 1.0
CG2 C:VAL533 4.8 20.5 1.0
CA C:ASP674 4.8 23.6 1.0
O C:ASP674 4.9 23.7 1.0

Zinc binding site 4 out of 4 in 5sji

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Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- Chloro-2-Methyl-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-Methyl-N-(2-Phenyl-1H-Benzimidazol-5-Yl)Pyrazole-3- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:32.7
occ:1.00
 O D:HOH928 2.0 23.1 1.0
NE2 D:HIS563 2.1 25.7 1.0
NE2 D:HIS529 2.2 34.0 1.0
O D:HOH958 2.2 40.9 1.0
OD1 D:ASP674 2.2 27.6 1.0
OD2 D:ASP564 2.3 27.7 1.0
CD2 D:HIS563 3.0 24.6 1.0
CG D:ASP674 3.1 28.8 1.0
CD2 D:HIS529 3.1 33.3 1.0
CE1 D:HIS529 3.1 31.6 1.0
OD2 D:ASP674 3.2 29.1 1.0
CG D:ASP564 3.2 29.2 1.0
CE1 D:HIS563 3.3 25.6 1.0
OD1 D:ASP564 3.7 31.8 1.0
MG D:MG802 3.8 31.2 1.0
CD2 D:HIS525 4.0 32.7 1.0
O D:HOH961 4.2 25.8 1.0
CG D:HIS563 4.2 24.3 1.0
ND1 D:HIS529 4.2 29.1 1.0
CG D:HIS529 4.3 30.3 1.0
ND1 D:HIS563 4.3 23.1 1.0
NE2 D:HIS525 4.3 36.0 1.0
O D:HOH934 4.3 30.3 1.0
CB D:ASP564 4.4 26.9 1.0
CB D:ASP674 4.5 27.1 1.0
O D:HOH939 4.7 29.8 1.0
CG2 D:VAL533 4.7 28.0 1.0
O D:ASP674 4.8 28.0 1.0
CA D:ASP674 4.8 27.4 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 06:02:37 2024

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