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Zinc in PDB 5shu: Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole:
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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole, PDB code: 5shu 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) 43.64 / 1.98
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.672, 135.672, 235.693, 90, 90, 120
R / Rfree (%) 18.8 / 22.1

Other elements in 5shu:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 2-[(4- Methoxy-3,5-Dimethylpyridin-2-Yl)Methylsulfanyl]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole 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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole (pdb code 5shu). 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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole, PDB code: 5shu:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shu

Go back to Zinc Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole


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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:25.8
occ:1.00
 NE2 A:HIS563 2.1 21.4 1.0
O A:HOH945 2.1 20.5 1.0
NE2 A:HIS529 2.1 20.8 1.0
OD2 A:ASP564 2.2 21.3 1.0
OD1 A:ASP674 2.2 24.9 1.0
O A:HOH1006 2.3 32.4 1.0
CD2 A:HIS563 3.0 21.0 1.0
CG A:ASP674 3.0 25.4 1.0
CE1 A:HIS529 3.1 20.6 1.0
CG A:ASP564 3.1 22.0 1.0
CD2 A:HIS529 3.1 21.6 1.0
CE1 A:HIS563 3.1 21.4 1.0
OD2 A:ASP674 3.3 28.8 1.0
OD1 A:ASP564 3.6 21.7 1.0
MG A:MG802 3.7 20.9 1.0
O A:HOH1031 4.1 19.4 1.0
CD2 A:HIS525 4.1 25.4 1.0
CG A:HIS563 4.2 21.2 1.0
ND1 A:HIS563 4.2 20.5 1.0
ND1 A:HIS529 4.2 19.7 1.0
CG A:HIS529 4.2 20.8 1.0
O A:HOH970 4.2 30.4 1.0
CB A:ASP564 4.3 21.2 1.0
CB A:ASP674 4.4 23.5 1.0
NE2 A:HIS525 4.5 26.3 1.0
O A:HOH930 4.5 19.7 1.0
CG2 A:VAL533 4.7 22.3 1.0
CA A:ASP674 4.9 22.8 1.0
O A:ASP674 4.9 21.8 1.0

Zinc binding site 2 out of 4 in 5shu

Go back to Zinc Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole


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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:24.7
occ:1.00
 NE2 B:HIS563 2.1 16.8 1.0
O B:HOH926 2.1 20.6 1.0
OD2 B:ASP564 2.1 20.2 1.0
OD1 B:ASP674 2.1 21.6 1.0
NE2 B:HIS529 2.2 21.2 1.0
O B:HOH1003 2.2 26.9 1.0
CD2 B:HIS563 3.0 18.9 1.0
CG B:ASP674 3.0 23.1 1.0
CE1 B:HIS563 3.1 17.7 1.0
CG B:ASP564 3.1 19.9 1.0
CD2 B:HIS529 3.1 21.1 1.0
CE1 B:HIS529 3.2 22.1 1.0
OD2 B:ASP674 3.3 23.0 1.0
OD1 B:ASP564 3.6 20.6 1.0
MG B:MG802 3.8 19.4 1.0
O B:HOH1031 4.0 20.6 1.0
O B:HOH992 4.1 31.9 1.0
CD2 B:HIS525 4.1 24.9 1.0
CG B:HIS563 4.2 18.4 1.0
ND1 B:HIS563 4.2 18.0 1.0
ND1 B:HIS529 4.3 21.8 1.0
CG B:HIS529 4.3 22.1 1.0
CB B:ASP564 4.3 18.8 1.0
CB B:ASP674 4.4 23.3 1.0
NE2 B:HIS525 4.4 25.1 1.0
O B:HOH941 4.5 17.6 1.0
CG2 B:VAL533 4.6 19.5 1.0
CA B:ASP674 4.8 22.7 1.0
O B:ASP674 4.9 19.9 1.0
O B:HOH1067 5.0 45.0 1.0

Zinc binding site 3 out of 4 in 5shu

Go back to Zinc Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole


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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:27.8
occ:1.00
 NE2 C:HIS563 2.1 19.3 1.0
O C:HOH973 2.1 24.9 1.0
O C:HOH1027 2.2 31.3 1.0
NE2 C:HIS529 2.2 22.3 1.0
OD2 C:ASP564 2.2 22.4 1.0
OD1 C:ASP674 2.2 23.3 1.0
CD2 C:HIS563 3.0 20.3 1.0
CD2 C:HIS529 3.1 24.1 1.0
CG C:ASP674 3.1 24.1 1.0
CE1 C:HIS563 3.1 20.2 1.0
CG C:ASP564 3.2 23.6 1.0
CE1 C:HIS529 3.2 25.3 1.0
OD2 C:ASP674 3.3 27.5 1.0
OD1 C:ASP564 3.7 23.5 1.0
MG C:MG802 3.8 23.8 1.0
O C:HOH1028 4.1 21.1 1.0
CD2 C:HIS525 4.1 28.3 1.0
CG C:HIS563 4.1 19.7 1.0
ND1 C:HIS563 4.2 19.4 1.0
O C:HOH1022 4.3 39.3 1.0
CG C:HIS529 4.3 24.6 1.0
ND1 C:HIS529 4.3 24.2 1.0
CB C:ASP564 4.3 22.8 1.0
CB C:ASP674 4.5 25.1 1.0
NE2 C:HIS525 4.5 29.2 1.0
O C:HOH935 4.6 23.8 1.0
CG2 C:VAL533 4.7 22.2 1.0
CA C:ASP674 4.8 24.3 1.0
O C:HOH1065 4.9 48.9 1.0
O C:ASP674 4.9 25.0 1.0

Zinc binding site 4 out of 4 in 5shu

Go back to Zinc Binding Sites List in 5shu
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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole


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]-3,5,6,7- Tetrahydropyrrolo[3,2-F]Benzimidazole within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:33.5
occ:1.00
 O D:HOH924 2.0 25.7 1.0
NE2 D:HIS563 2.1 26.6 1.0
NE2 D:HIS529 2.1 34.4 1.0
OD2 D:ASP564 2.1 30.3 1.0
O D:HOH964 2.2 35.5 1.0
OD1 D:ASP674 2.2 28.7 1.0
CD2 D:HIS563 3.0 27.9 1.0
CD2 D:HIS529 3.0 33.8 1.0
CG D:ASP674 3.1 30.4 1.0
CG D:ASP564 3.1 28.5 1.0
CE1 D:HIS563 3.1 27.3 1.0
CE1 D:HIS529 3.2 34.4 1.0
OD2 D:ASP674 3.3 29.4 1.0
OD1 D:ASP564 3.6 28.2 1.0
MG D:MG802 3.8 29.0 1.0
CD2 D:HIS525 4.0 32.2 1.0
O D:HOH989 4.1 28.6 1.0
CG D:HIS563 4.2 26.4 1.0
ND1 D:HIS563 4.2 27.5 1.0
CG D:HIS529 4.2 32.2 1.0
O D:HOH967 4.2 43.0 1.0
ND1 D:HIS529 4.3 30.7 1.0
CB D:ASP564 4.3 29.2 1.0
NE2 D:HIS525 4.4 32.8 1.0
CB D:ASP674 4.5 29.4 1.0
O D:HOH912 4.6 27.3 1.0
CG2 D:VAL533 4.7 30.1 1.0
O D:ASP674 4.9 31.1 1.0
CA D:ASP674 4.9 30.1 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: Mon Oct 28 05:35:35 2024

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