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Zinc in PDB 5sk6: Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sk6 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) 43.60 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.196, 135.196, 234.886, 90, 90, 120
R / Rfree (%) 18.8 / 23.3

Other elements in 5sk6:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-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 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide (pdb code 5sk6). 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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide, PDB code: 5sk6:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sk6

Go back to Zinc Binding Sites List in 5sk6
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:36.9
occ:1.00
 NE2 A:HIS563 2.1 28.9 1.0
NE2 A:HIS529 2.1 33.1 1.0
OD2 A:ASP564 2.1 31.2 1.0
O A:HOH955 2.2 27.4 1.0
OD1 A:ASP674 2.2 36.4 1.0
O A:HOH970 2.4 37.5 1.0
CD2 A:HIS563 3.0 31.9 1.0
CE1 A:HIS529 3.0 32.0 1.0
CD2 A:HIS529 3.1 32.1 1.0
CE1 A:HIS563 3.1 30.9 1.0
CG A:ASP674 3.1 32.8 1.0
CG A:ASP564 3.1 30.8 1.0
OD2 A:ASP674 3.3 41.2 1.0
OD1 A:ASP564 3.6 27.7 1.0
MG A:MG802 3.8 27.2 1.0
CG A:HIS563 4.1 31.8 1.0
ND1 A:HIS529 4.1 30.7 1.0
ND1 A:HIS563 4.1 29.9 1.0
O A:HOH988 4.2 27.3 1.0
CG A:HIS529 4.2 30.2 1.0
CD2 A:HIS525 4.2 32.4 1.0
CB A:ASP564 4.3 29.9 1.0
O A:HOH967 4.3 39.2 1.0
CB A:ASP674 4.4 33.7 1.0
NE2 A:HIS525 4.6 33.0 1.0
O A:HOH913 4.6 22.3 1.0
CG2 A:VAL533 4.8 28.1 1.0
CA A:ASP674 4.9 30.9 1.0
O A:ASP674 4.9 32.7 1.0

Zinc binding site 2 out of 4 in 5sk6

Go back to Zinc Binding Sites List in 5sk6
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.1
occ:1.00
 OD2 B:ASP564 2.1 32.0 1.0
NE2 B:HIS563 2.2 28.2 1.0
OD1 B:ASP674 2.2 31.0 1.0
NE2 B:HIS529 2.2 27.0 1.0
O B:HOH950 2.2 28.4 1.0
O B:HOH960 2.4 40.5 1.0
CG B:ASP674 3.0 31.1 1.0
CD2 B:HIS563 3.1 29.6 1.0
CD2 B:HIS529 3.1 28.3 1.0
CG B:ASP564 3.1 30.5 1.0
CE1 B:HIS563 3.2 27.0 1.0
OD2 B:ASP674 3.2 32.2 1.0
CE1 B:HIS529 3.2 29.0 1.0
OD1 B:ASP564 3.6 30.0 1.0
MG B:MG802 3.8 26.2 1.0
O B:HOH972 4.1 26.3 1.0
CD2 B:HIS525 4.1 34.7 1.0
CG B:HIS563 4.2 28.6 1.0
ND1 B:HIS563 4.2 27.1 1.0
O B:HOH989 4.3 39.9 1.0
CG B:HIS529 4.3 28.0 1.0
CB B:ASP564 4.3 30.1 1.0
ND1 B:HIS529 4.3 28.4 1.0
CB B:ASP674 4.4 30.4 1.0
NE2 B:HIS525 4.4 37.0 1.0
O B:HOH947 4.6 27.6 1.0
O B:HOH1009 4.6 56.7 1.0
O B:ASP674 4.8 28.5 1.0
CA B:ASP674 4.8 29.3 1.0
CG2 B:VAL533 4.8 27.8 1.0

Zinc binding site 3 out of 4 in 5sk6

Go back to Zinc Binding Sites List in 5sk6
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:33.1
occ:1.00
 O C:HOH987 2.1 41.2 1.0
O C:HOH914 2.1 24.4 1.0
OD2 C:ASP564 2.1 27.9 1.0
NE2 C:HIS529 2.1 29.6 1.0
OD1 C:ASP674 2.2 31.5 1.0
NE2 C:HIS563 2.2 29.6 1.0
CG C:ASP674 3.0 30.7 1.0
CD2 C:HIS563 3.1 26.9 1.0
CD2 C:HIS529 3.1 31.2 1.0
CG C:ASP564 3.1 28.2 1.0
CE1 C:HIS529 3.2 31.2 1.0
OD2 C:ASP674 3.2 30.3 1.0
CE1 C:HIS563 3.3 28.1 1.0
OD1 C:ASP564 3.6 27.9 1.0
MG C:MG802 3.7 29.4 1.0
CD2 C:HIS525 4.1 37.1 1.0
O C:HOH999 4.2 30.7 1.0
CG C:HIS529 4.2 32.5 1.0
ND1 C:HIS529 4.2 31.7 1.0
CG C:HIS563 4.3 26.4 1.0
CB C:ASP564 4.3 26.2 1.0
O C:HOH990 4.3 44.4 1.0
ND1 C:HIS563 4.4 25.7 1.0
CB C:ASP674 4.4 29.2 1.0
NE2 C:HIS525 4.5 37.2 1.0
O C:HOH929 4.6 31.4 1.0
O C:HOH1009 4.7 51.8 1.0
CA C:ASP674 4.8 31.2 1.0
CG2 C:VAL533 4.8 32.4 1.0
O C:ASP674 4.9 31.0 1.0

Zinc binding site 4 out of 4 in 5sk6

Go back to Zinc Binding Sites List in 5sk6
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 4- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-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- (Azetidine-1-Carbonyl)-N-[3-(1,3-Benzoxazol-2-Yl)Phenyl]-2- Methylpyrazole-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:52.8
occ:1.00
 NE2 D:HIS529 2.1 45.1 1.0
O D:HOH932 2.1 36.3 1.0
NE2 D:HIS563 2.2 39.9 1.0
OD2 D:ASP564 2.3 49.0 1.0
OD1 D:ASP674 2.3 47.2 1.0
O D:HOH944 2.3 45.7 1.0
CD2 D:HIS563 3.0 40.9 1.0
CD2 D:HIS529 3.1 49.1 1.0
CE1 D:HIS529 3.2 45.0 1.0
CG D:ASP564 3.2 45.5 1.0
CG D:ASP674 3.2 46.9 1.0
CE1 D:HIS563 3.2 41.0 1.0
OD2 D:ASP674 3.5 50.0 1.0
OD1 D:ASP564 3.7 47.4 1.0
MG D:MG802 3.9 49.1 1.0
O D:HOH931 4.1 43.9 1.0
CG D:HIS563 4.2 41.9 1.0
CD2 D:HIS525 4.2 58.5 1.0
O D:HOH925 4.3 49.1 1.0
ND1 D:HIS529 4.3 47.9 1.0
CG D:HIS529 4.3 46.2 1.0
ND1 D:HIS563 4.3 41.8 1.0
CB D:ASP564 4.3 46.7 1.0
O D:HOH912 4.4 41.3 1.0
CB D:ASP674 4.5 49.8 1.0
O D:ASP674 4.7 52.4 1.0
NE2 D:HIS525 4.7 58.9 1.0
CG2 D:VAL533 4.7 45.5 1.0
CA D:ASP674 4.8 49.1 1.0
O D:HOH916 5.0 40.3 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 06:13:57 2024

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