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Zinc in PDB 5shf: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide, PDB code: 5shf was solved by C.Joseph, J.Benz, A.Flohr, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.73 / 2.28
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 136.132, 136.132, 235.418, 90, 90, 120
R / Rfree (%) 17.4 / 22.3

Other elements in 5shf:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide (pdb code 5shf). 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide, PDB code: 5shf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shf

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Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.3
occ:1.00
 NE2 A:HIS563 2.0 30.1 1.0
OD2 A:ASP564 2.1 36.2 1.0
OD1 A:ASP674 2.1 37.9 1.0
O A:HOH955 2.2 30.1 1.0
NE2 A:HIS529 2.2 36.1 1.0
O A:HOH988 2.9 37.9 1.0
CD2 A:HIS563 3.0 31.2 1.0
CE1 A:HIS563 3.0 29.0 1.0
CG A:ASP674 3.0 36.8 1.0
CG A:ASP564 3.1 31.4 1.0
CE1 A:HIS529 3.1 33.1 1.0
CD2 A:HIS529 3.2 33.7 1.0
OD2 A:ASP674 3.3 44.1 1.0
OD1 A:ASP564 3.6 29.0 1.0
MG A:MG802 3.8 33.0 1.0
O A:HOH1005 4.1 29.5 1.0
ND1 A:HIS563 4.1 28.1 1.0
CG A:HIS563 4.1 29.0 1.0
CD2 A:HIS525 4.2 33.8 1.0
ND1 A:HIS529 4.3 34.5 1.0
O A:HOH978 4.3 44.0 1.0
CB A:ASP564 4.3 28.9 1.0
CG A:HIS529 4.3 32.4 1.0
CB A:ASP674 4.4 33.5 1.0
NE2 A:HIS525 4.6 33.0 1.0
O A:HOH924 4.6 31.1 1.0
CG2 A:VAL533 4.7 29.0 1.0
O A:HOH1019 4.8 47.9 1.0
CA A:ASP674 4.8 32.4 1.0
O A:ASP674 4.8 32.1 1.0

Zinc binding site 2 out of 4 in 5shf

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Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:36.1
occ:1.00
 NE2 B:HIS563 2.1 28.5 1.0
OD2 B:ASP564 2.2 27.8 1.0
O B:HOH954 2.2 26.9 1.0
NE2 B:HIS529 2.2 26.1 1.0
OD1 B:ASP674 2.2 28.7 1.0
O B:HOH972 2.5 41.6 1.0
CD2 B:HIS563 3.1 28.5 1.0
CG B:ASP674 3.1 30.7 1.0
CE1 B:HIS563 3.1 29.3 1.0
CG B:ASP564 3.1 26.4 1.0
CD2 B:HIS529 3.2 29.9 1.0
CE1 B:HIS529 3.2 31.2 1.0
OD2 B:ASP674 3.3 36.1 1.0
OD1 B:ASP564 3.5 28.8 1.0
MG B:MG802 3.8 31.8 1.0
O B:HOH997 4.0 26.0 1.0
CD2 B:HIS525 4.2 29.9 1.0
CG B:HIS563 4.2 28.3 1.0
ND1 B:HIS563 4.2 26.4 1.0
O B:HOH976 4.3 41.7 1.0
CG B:HIS529 4.3 31.2 1.0
ND1 B:HIS529 4.3 30.0 1.0
CB B:ASP564 4.4 27.0 1.0
CB B:ASP674 4.4 30.7 1.0
NE2 B:HIS525 4.5 28.5 1.0
O B:HOH948 4.6 31.0 1.0
O B:ASP674 4.7 31.0 1.0
CG2 B:VAL533 4.8 29.7 1.0
CA B:ASP674 4.9 29.6 1.0

Zinc binding site 3 out of 4 in 5shf

Go back to Zinc Binding Sites List in 5shf
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:35.4
occ:1.00
 O C:HOH962 2.0 27.2 1.0
NE2 C:HIS563 2.1 30.7 1.0
OD2 C:ASP564 2.1 29.7 1.0
NE2 C:HIS529 2.1 33.4 1.0
OD1 C:ASP674 2.2 31.6 1.0
O C:HOH974 2.4 38.4 1.0
CG C:ASP674 3.0 30.4 1.0
CD2 C:HIS563 3.0 28.9 1.0
CE1 C:HIS529 3.1 33.5 1.0
OD2 C:ASP674 3.1 29.7 1.0
CD2 C:HIS529 3.2 31.9 1.0
CE1 C:HIS563 3.2 30.4 1.0
CG C:ASP564 3.2 30.5 1.0
OD1 C:ASP564 3.7 28.7 1.0
MG C:MG802 3.8 32.8 1.0
CD2 C:HIS525 4.1 35.0 1.0
O C:HOH1016 4.1 40.5 1.0
CG C:HIS563 4.2 29.7 1.0
ND1 C:HIS529 4.2 34.3 1.0
O C:HOH1007 4.2 33.1 1.0
ND1 C:HIS563 4.2 28.5 1.0
CG C:HIS529 4.3 30.6 1.0
CB C:ASP564 4.4 29.7 1.0
NE2 C:HIS525 4.4 36.4 1.0
CB C:ASP674 4.4 31.8 1.0
O C:HOH961 4.5 30.4 1.0
O C:HOH1036 4.7 43.5 1.0
O C:ASP674 4.9 34.0 1.0
CA C:ASP674 4.9 31.9 1.0
CG2 C:VAL533 4.9 32.7 1.0

Zinc binding site 4 out of 4 in 5shf

Go back to Zinc Binding Sites List in 5shf
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- 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 3,6- Dimethyl-N-(2-Phenylpyrazolo[1,5-A]Pyridin-6-Yl)Pyridine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:51.0
occ:1.00
 NE2 D:HIS563 2.0 34.1 1.0
OD1 D:ASP674 2.1 54.6 1.0
O D:HOH920 2.2 35.8 1.0
NE2 D:HIS529 2.2 46.1 1.0
O D:HOH944 2.3 47.1 1.0
OD2 D:ASP564 2.4 45.4 1.0
CD2 D:HIS563 3.0 38.4 1.0
CG D:ASP674 3.0 49.1 1.0
CE1 D:HIS563 3.1 39.5 1.0
CD2 D:HIS529 3.2 48.0 1.0
CG D:ASP564 3.2 42.4 1.0
CE1 D:HIS529 3.3 46.2 1.0
OD2 D:ASP674 3.3 50.5 1.0
OD1 D:ASP564 3.7 43.7 1.0
MG D:MG802 4.0 45.3 1.0
O D:HOH922 4.0 49.8 1.0
CG D:HIS563 4.2 39.1 1.0
O D:HOH943 4.2 35.0 1.0
ND1 D:HIS563 4.2 38.1 1.0
CB D:ASP564 4.3 45.1 1.0
CD2 D:HIS525 4.3 47.3 1.0
CG D:HIS529 4.3 46.1 1.0
ND1 D:HIS529 4.4 50.1 1.0
CB D:ASP674 4.4 50.0 1.0
CG2 D:VAL533 4.7 46.6 1.0
O D:ASP674 4.8 51.9 1.0
O D:HOH906 4.8 43.4 1.0
NE2 D:HIS525 4.8 47.4 1.0
CA D:ASP674 4.8 47.7 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 05:31:00 2024

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