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Zinc in PDB 5sh7: Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5sh7 was solved by C.Joseph, J.Benz, A.Flohr, K.Bleicher, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.57 / 2.66
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.448, 135.448, 236.063, 90, 90, 120
R / Rfree (%) 17.7 / 25.3

Other elements in 5sh7:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide 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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide (pdb code 5sh7). 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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide, PDB code: 5sh7:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sh7

Go back to Zinc Binding Sites List in 5sh7
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:40.5
occ:1.00
 OD2 A:ASP564 2.1 41.8 1.0
NE2 A:HIS529 2.2 36.6 1.0
O A:HOH924 2.2 37.7 1.0
NE2 A:HIS563 2.2 29.9 1.0
OD1 A:ASP674 2.3 39.3 1.0
O A:HOH907 2.7 30.7 1.0
CE1 A:HIS563 3.1 32.9 1.0
CD2 A:HIS529 3.1 34.7 1.0
CG A:ASP674 3.1 37.7 1.0
CG A:ASP564 3.1 35.1 1.0
CE1 A:HIS529 3.1 36.2 1.0
CD2 A:HIS563 3.2 35.4 1.0
OD2 A:ASP674 3.3 44.2 1.0
OD1 A:ASP564 3.6 34.4 1.0
MG A:MG802 3.8 41.7 1.0
O A:HOH993 4.0 44.8 1.0
O A:HOH944 4.1 39.0 1.0
CD2 A:HIS525 4.1 36.9 1.0
ND1 A:HIS563 4.2 32.1 1.0
ND1 A:HIS529 4.2 37.4 1.0
CG A:HIS529 4.2 35.2 1.0
CG A:HIS563 4.3 35.2 1.0
CB A:ASP564 4.3 31.6 1.0
NE2 A:HIS525 4.4 35.9 1.0
CB A:ASP674 4.5 36.1 1.0
O A:HOH938 4.6 34.1 1.0
CG2 A:VAL533 4.8 35.3 1.0
O A:ASP674 4.8 35.8 1.0
CA A:ASP674 4.9 36.3 1.0

Zinc binding site 2 out of 4 in 5sh7

Go back to Zinc Binding Sites List in 5sh7
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:39.8
occ:1.00
 NE2 B:HIS563 2.2 34.0 1.0
NE2 B:HIS529 2.2 38.2 1.0
OD1 B:ASP674 2.2 43.7 1.0
O B:HOH919 2.4 34.6 1.0
OD2 B:ASP564 2.4 38.0 1.0
O B:HOH905 2.6 40.9 1.0
CD2 B:HIS529 3.1 36.9 1.0
CD2 B:HIS563 3.1 34.9 1.0
CE1 B:HIS563 3.1 36.3 1.0
CG B:ASP674 3.1 36.7 1.0
CG B:ASP564 3.3 35.6 1.0
CE1 B:HIS529 3.3 41.9 1.0
OD2 B:ASP674 3.4 41.8 1.0
OD1 B:ASP564 3.6 36.5 1.0
O B:HOH975 3.7 44.0 1.0
MG B:MG802 4.0 36.0 1.0
O B:HOH997 4.0 47.9 1.0
CD2 B:HIS525 4.1 39.9 1.0
ND1 B:HIS563 4.2 35.5 1.0
CG B:HIS563 4.3 33.3 1.0
CG B:HIS529 4.3 39.1 1.0
NE2 B:HIS525 4.3 36.2 1.0
ND1 B:HIS529 4.3 37.4 1.0
O B:HOH917 4.4 34.6 1.0
CB B:ASP564 4.4 32.6 1.0
CB B:ASP674 4.5 31.9 1.0
CG2 B:VAL533 4.8 35.5 1.0
CA B:ASP674 4.9 37.1 1.0
O B:HOH939 5.0 35.3 1.0

Zinc binding site 3 out of 4 in 5sh7

Go back to Zinc Binding Sites List in 5sh7
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:41.8
occ:1.00
 O C:HOH939 2.1 37.1 1.0
NE2 C:HIS529 2.1 36.0 1.0
OD1 C:ASP674 2.1 37.8 1.0
OD2 C:ASP564 2.3 38.9 1.0
NE2 C:HIS563 2.4 33.3 1.0
O C:HOH915 2.6 39.2 1.0
CD2 C:HIS529 3.1 36.8 1.0
CG C:ASP674 3.1 35.5 1.0
CE1 C:HIS529 3.2 37.8 1.0
CD2 C:HIS563 3.2 34.1 1.0
CG C:ASP564 3.3 36.8 1.0
OD2 C:ASP674 3.3 43.8 1.0
CE1 C:HIS563 3.4 33.2 1.0
OD1 C:ASP564 3.7 42.5 1.0
MG C:MG802 3.8 43.7 1.0
O C:HOH967 3.8 41.7 1.0
CD2 C:HIS525 3.9 41.9 1.0
NE2 C:HIS525 4.2 36.9 1.0
O C:HOH925 4.2 31.7 1.0
CG C:HIS529 4.3 35.8 1.0
ND1 C:HIS529 4.3 32.9 1.0
CG C:HIS563 4.4 34.1 1.0
ND1 C:HIS563 4.4 30.0 1.0
CB C:ASP564 4.5 27.7 1.0
CB C:ASP674 4.5 37.2 1.0
O C:HOH917 4.6 37.3 1.0
CG2 C:VAL533 4.7 35.6 1.0
CA C:ASP674 4.8 40.7 1.0
O C:ASP674 4.9 39.7 1.0
O C:HOH1014 4.9 46.9 1.0

Zinc binding site 4 out of 4 in 5sh7

Go back to Zinc Binding Sites List in 5sh7
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-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 6-[(5- Cyclopropyl-2-Oxo-1H-Pyridine-3-Carbonyl)Amino]-N-(Oxetan-3-Yl)-2- Phenyl-3H-Benzimidazole-5-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:52.6
occ:1.00
 NE2 D:HIS563 2.1 39.4 1.0
OD1 D:ASP674 2.2 54.1 1.0
OD2 D:ASP564 2.4 51.6 1.0
NE2 D:HIS529 2.4 50.1 1.0
O D:HOH945 2.5 52.6 1.0
O D:HOH903 2.7 40.2 1.0
CD2 D:HIS563 2.9 41.4 1.0
CG D:ASP674 3.0 50.0 1.0
CE1 D:HIS563 3.1 40.8 1.0
CG D:ASP564 3.2 47.0 1.0
CD2 D:HIS529 3.3 48.2 1.0
OD2 D:ASP674 3.3 51.9 1.0
CE1 D:HIS529 3.4 50.2 1.0
O D:HOH958 3.6 52.4 1.0
OD1 D:ASP564 3.8 47.9 1.0
CG D:HIS563 4.1 44.6 1.0
ND1 D:HIS563 4.1 44.3 1.0
ND1 D:HIS525 4.2 56.8 1.0
CB D:ASP564 4.2 44.3 1.0
CE1 D:HIS525 4.3 54.8 1.0
O D:HOH926 4.4 40.7 1.0
CB D:ASP674 4.4 53.1 1.0
CG D:HIS529 4.5 52.2 1.0
O D:HOH912 4.5 55.5 1.0
ND1 D:HIS529 4.5 48.7 1.0
MG D:MG802 4.5 55.9 1.0
O D:ASP674 4.7 55.9 1.0
O D:HOH929 4.7 49.8 1.0
CG2 D:VAL533 4.8 45.7 1.0
CA D:ASP674 4.9 52.1 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: Fri Apr 7 22:19:07 2023

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