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Zinc in PDB 5sjm: Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One, PDB code: 5sjm 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) 43.22 / 2.30
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.799, 134.799, 232.623, 90, 90, 120
R / Rfree (%) 18.4 / 24.2

Other elements in 5sjm:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One 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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One (pdb code 5sjm). 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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One, PDB code: 5sjm:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjm

Go back to Zinc Binding Sites List in 5sjm
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:37.9
occ:1.00
 OD2 A:ASP564 2.0 36.2 1.0
NE2 A:HIS563 2.0 28.8 1.0
NE2 A:HIS529 2.1 36.0 1.0
OD1 A:ASP674 2.1 38.6 1.0
O A:HOH957 2.1 48.4 1.0
O A:HOH915 2.3 30.0 1.0
CG A:ASP674 2.9 37.4 1.0
CD2 A:HIS563 3.0 31.0 1.0
CE1 A:HIS529 3.0 37.1 1.0
CD2 A:HIS529 3.1 35.5 1.0
CG A:ASP564 3.1 32.2 1.0
CE1 A:HIS563 3.1 32.8 1.0
OD2 A:ASP674 3.2 45.3 1.0
OD1 A:ASP564 3.6 32.0 1.0
MG A:MG802 3.8 28.7 1.0
CG A:HIS563 4.1 30.7 1.0
ND1 A:HIS529 4.2 35.5 1.0
ND1 A:HIS563 4.2 30.6 1.0
CG A:HIS529 4.2 32.9 1.0
CB A:ASP564 4.2 28.2 1.0
CD2 A:HIS525 4.2 34.4 1.0
O A:HOH967 4.3 31.7 1.0
CB A:ASP674 4.3 36.4 1.0
O A:HOH904 4.5 24.3 1.0
NE2 A:HIS525 4.6 35.3 1.0
CG2 A:VAL533 4.6 29.5 1.0
CA A:ASP674 4.8 33.2 1.0
O A:HOH929 5.0 26.6 1.0
O A:ASP674 5.0 39.1 1.0

Zinc binding site 2 out of 4 in 5sjm

Go back to Zinc Binding Sites List in 5sjm
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.9
occ:1.00
 NE2 B:HIS529 2.0 35.0 1.0
OD2 B:ASP564 2.0 33.0 1.0
NE2 B:HIS563 2.1 27.9 1.0
O B:HOH921 2.1 20.4 1.0
OD1 B:ASP674 2.2 36.7 1.0
O B:HOH934 2.4 36.7 1.0
CG B:ASP674 3.0 34.6 1.0
CD2 B:HIS529 3.0 31.1 1.0
CE1 B:HIS529 3.1 32.1 1.0
CD2 B:HIS563 3.1 26.4 1.0
CG B:ASP564 3.1 30.0 1.0
CE1 B:HIS563 3.1 30.1 1.0
OD2 B:ASP674 3.1 36.1 1.0
OD1 B:ASP564 3.6 30.9 1.0
O B:HOH936 4.0 49.0 1.0
MG B:MG802 4.0 28.4 1.0
O B:HOH947 4.0 24.6 1.0
CG B:HIS529 4.1 30.5 1.0
ND1 B:HIS529 4.1 30.0 1.0
CD2 B:HIS525 4.2 34.3 1.0
CG B:HIS563 4.2 26.4 1.0
ND1 B:HIS563 4.2 28.0 1.0
CB B:ASP564 4.2 28.3 1.0
CB B:ASP674 4.4 32.0 1.0
NE2 B:HIS525 4.4 34.1 1.0
O B:HOH913 4.6 29.3 1.0
CG2 B:VAL533 4.6 25.3 1.0
CA B:ASP674 4.8 30.9 1.0
O B:ASP674 4.9 34.5 1.0

Zinc binding site 3 out of 4 in 5sjm

Go back to Zinc Binding Sites List in 5sjm
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:37.1
occ:1.00
 OD2 C:ASP564 2.0 31.8 1.0
O C:HOH926 2.1 32.0 1.0
OD1 C:ASP674 2.1 35.8 1.0
NE2 C:HIS563 2.1 28.3 1.0
NE2 C:HIS529 2.1 34.7 1.0
CG C:ASP674 3.0 35.1 1.0
CD2 C:HIS563 3.0 27.4 1.0
CE1 C:HIS529 3.0 33.5 1.0
CG C:ASP564 3.1 29.2 1.0
CE1 C:HIS563 3.1 30.4 1.0
CD2 C:HIS529 3.2 29.9 1.0
OD2 C:ASP674 3.2 37.8 1.0
OD1 C:ASP564 3.6 31.6 1.0
MG C:MG802 3.7 32.3 1.0
CD2 C:HIS525 4.1 41.7 1.0
ND1 C:HIS529 4.2 30.9 1.0
CG C:HIS563 4.2 27.6 1.0
ND1 C:HIS563 4.2 29.5 1.0
O C:HOH965 4.2 30.8 1.0
CG C:HIS529 4.3 29.6 1.0
CB C:ASP564 4.3 26.8 1.0
NE2 C:HIS525 4.4 45.0 1.0
CB C:ASP674 4.4 35.0 1.0
O C:HOH918 4.5 27.0 1.0
CA C:ASP674 4.8 34.6 1.0
CG2 C:VAL533 4.8 25.3 1.0
O C:HOH942 4.9 28.0 1.0
O C:ASP674 4.9 39.7 1.0

Zinc binding site 4 out of 4 in 5sjm

Go back to Zinc Binding Sites List in 5sjm
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One


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-(2- Phenylethyl)-5-Pyridin-4-Yl-1H-Pyridin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:56.0
occ:1.00
 NE2 D:HIS563 1.9 41.4 1.0
O D:HOH914 2.1 35.4 1.0
NE2 D:HIS529 2.1 47.9 1.0
OD2 D:ASP564 2.2 58.1 1.0
O D:HOH911 2.2 36.0 1.0
OD1 D:ASP674 2.2 49.8 1.0
CD2 D:HIS563 2.8 44.2 1.0
CE1 D:HIS563 3.0 42.3 1.0
CG D:ASP674 3.1 52.0 1.0
CD2 D:HIS529 3.1 50.8 1.0
CE1 D:HIS529 3.1 50.5 1.0
CG D:ASP564 3.1 48.8 1.0
OD2 D:ASP674 3.3 61.4 1.0
OD1 D:ASP564 3.7 55.0 1.0
MG D:MG802 3.8 51.0 1.0
CG D:HIS563 4.0 43.7 1.0
ND1 D:HIS563 4.1 42.4 1.0
CB D:ASP564 4.1 46.1 1.0
O D:HOH921 4.2 42.7 1.0
ND1 D:HIS529 4.2 55.1 1.0
CG D:HIS529 4.2 51.5 1.0
CD2 D:HIS525 4.3 55.0 1.0
O D:HOH905 4.4 53.9 1.0
CB D:ASP674 4.4 55.5 1.0
CG2 D:VAL533 4.7 50.3 1.0
NE2 D:HIS525 4.8 60.1 1.0
O D:ASP674 4.8 58.8 1.0
CA D:ASP674 4.9 57.0 1.0
O D:HOH907 4.9 48.7 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 06:02:37 2024

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