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Zinc in PDB 5sjb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline, PDB code: 5sjb was solved by C.Joseph, J.Benz, A.Flohr, A.Krasso, 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 (°) 135.538, 135.538, 235.689, 90, 90, 120
R / Rfree (%) 18.7 / 23.3

Other elements in 5sjb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline 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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline (pdb code 5sjb). 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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline, PDB code: 5sjb:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sjb

Go back to Zinc Binding Sites List in 5sjb
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:23.3
occ:1.00
 NE2 A:HIS563 2.0 18.1 1.0
OD2 A:ASP564 2.1 19.8 1.0
NE2 A:HIS529 2.1 21.2 1.0
O A:HOH913 2.2 20.9 1.0
OD1 A:ASP674 2.2 21.7 1.0
O A:HOH1015 2.4 30.9 1.0
CD2 A:HIS563 3.0 17.7 1.0
CE1 A:HIS563 3.0 19.4 1.0
CG A:ASP674 3.0 23.1 1.0
CG A:ASP564 3.1 18.6 1.0
CE1 A:HIS529 3.1 21.6 1.0
CD2 A:HIS529 3.1 21.4 1.0
OD2 A:ASP674 3.2 30.1 1.0
OD1 A:ASP564 3.6 18.0 1.0
MG A:MG802 3.7 17.6 1.0
O A:HOH1022 4.1 16.8 1.0
CG A:HIS563 4.1 18.2 1.0
ND1 A:HIS563 4.1 19.2 1.0
CD2 A:HIS525 4.2 24.1 1.0
ND1 A:HIS529 4.2 21.0 1.0
CB A:ASP564 4.2 19.0 1.0
O A:HOH976 4.3 31.8 1.0
CG A:HIS529 4.3 21.0 1.0
CB A:ASP674 4.4 22.2 1.0
NE2 A:HIS525 4.5 24.2 1.0
O A:HOH961 4.7 14.6 1.0
CG2 A:VAL533 4.7 17.3 1.0
CA A:ASP674 4.8 21.1 1.0
O A:ASP674 4.9 21.7 1.0

Zinc binding site 2 out of 4 in 5sjb

Go back to Zinc Binding Sites List in 5sjb
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.8
occ:1.00
 NE2 B:HIS563 2.0 16.2 1.0
OD2 B:ASP564 2.1 17.6 1.0
O B:HOH940 2.2 17.4 1.0
OD1 B:ASP674 2.2 22.2 1.0
NE2 B:HIS529 2.2 18.7 1.0
O B:HOH1004 2.3 32.0 1.0
CD2 B:HIS563 3.0 16.5 1.0
CG B:ASP674 3.0 22.7 1.0
CE1 B:HIS563 3.0 17.1 1.0
CG B:ASP564 3.1 17.6 1.0
CD2 B:HIS529 3.1 18.6 1.0
OD2 B:ASP674 3.2 23.4 1.0
CE1 B:HIS529 3.2 19.8 1.0
OD1 B:ASP564 3.5 16.5 1.0
MG B:MG802 3.8 13.7 1.0
O B:HOH982 4.0 15.4 1.0
CD2 B:HIS525 4.1 22.4 1.0
CG B:HIS563 4.1 16.2 1.0
ND1 B:HIS563 4.1 16.5 1.0
O B:HOH1002 4.2 31.4 1.0
CB B:ASP564 4.2 17.1 1.0
CG B:HIS529 4.3 19.7 1.0
ND1 B:HIS529 4.3 19.9 1.0
CB B:ASP674 4.4 22.3 1.0
NE2 B:HIS525 4.4 22.1 1.0
O B:HOH929 4.6 15.5 1.0
CG2 B:VAL533 4.7 18.5 1.0
CA B:ASP674 4.9 21.6 1.0
O B:ASP674 4.9 20.0 1.0

Zinc binding site 3 out of 4 in 5sjb

Go back to Zinc Binding Sites List in 5sjb
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:26.6
occ:1.00
 NE2 C:HIS563 2.1 18.8 1.0
O C:HOH959 2.1 18.3 1.0
OD2 C:ASP564 2.1 21.2 1.0
OD1 C:ASP674 2.1 21.8 1.0
NE2 C:HIS529 2.1 20.8 1.0
O C:HOH1027 2.3 31.5 1.0
CD2 C:HIS563 3.0 17.4 1.0
CG C:ASP674 3.0 23.9 1.0
CD2 C:HIS529 3.1 20.9 1.0
CG C:ASP564 3.1 20.1 1.0
CE1 C:HIS563 3.1 19.1 1.0
CE1 C:HIS529 3.2 21.3 1.0
OD2 C:ASP674 3.3 25.7 1.0
OD1 C:ASP564 3.6 19.4 1.0
MG C:MG802 3.9 20.6 1.0
O C:HOH1032 4.1 20.5 1.0
CG C:HIS563 4.2 18.2 1.0
CD2 C:HIS525 4.2 25.8 1.0
ND1 C:HIS563 4.2 17.3 1.0
CG C:HIS529 4.2 20.8 1.0
CB C:ASP564 4.3 19.2 1.0
ND1 C:HIS529 4.3 19.8 1.0
O C:HOH1020 4.4 42.3 1.0
CB C:ASP674 4.4 25.2 1.0
O C:HOH940 4.5 15.3 1.0
O C:HOH1050 4.5 51.2 1.0
NE2 C:HIS525 4.6 24.9 1.0
CG2 C:VAL533 4.7 18.2 1.0
CA C:ASP674 4.8 24.4 1.0
O C:ASP674 4.9 25.9 1.0

Zinc binding site 4 out of 4 in 5sjb

Go back to Zinc Binding Sites List in 5sjb
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline


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 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3H-Imidazo[4,5- F]Quinoline within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.8
occ:1.00
 NE2 D:HIS563 2.0 24.2 1.0
NE2 D:HIS529 2.1 32.2 1.0
O D:HOH937 2.1 25.4 1.0
O D:HOH967 2.2 38.4 1.0
OD2 D:ASP564 2.2 34.5 1.0
OD1 D:ASP674 2.3 31.8 1.0
CD2 D:HIS563 3.0 24.2 1.0
CE1 D:HIS563 3.1 26.3 1.0
CG D:ASP564 3.1 27.7 1.0
CG D:ASP674 3.1 32.4 1.0
CD2 D:HIS529 3.1 33.0 1.0
CE1 D:HIS529 3.1 33.9 1.0
OD2 D:ASP674 3.3 33.3 1.0
OD1 D:ASP564 3.6 26.6 1.0
MG D:MG802 3.8 28.3 1.0
O D:HOH989 4.1 30.3 1.0
O D:HOH971 4.1 46.7 1.0
CG D:HIS563 4.1 23.9 1.0
CD2 D:HIS525 4.2 33.0 1.0
ND1 D:HIS563 4.2 23.9 1.0
ND1 D:HIS529 4.2 31.9 1.0
CB D:ASP564 4.3 27.6 1.0
CG D:HIS529 4.3 31.1 1.0
O D:HOH947 4.5 22.9 1.0
CB D:ASP674 4.5 32.3 1.0
NE2 D:HIS525 4.6 32.7 1.0
CG2 D:VAL533 4.7 30.6 1.0
O D:ASP674 4.8 36.5 1.0
CA D:ASP674 4.9 31.4 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 05:58:45 2024

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