Zinc in PDB 5sj8: Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile, PDB code: 5sj8 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) 43.61 / 2.49
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.11, 135.11, 235.005, 90, 90, 120
R / Rfree (%) 16.6 / 20.1

Other elements in 5sj8:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile 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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile (pdb code 5sj8). 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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile, PDB code: 5sj8:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sj8

Go back to Zinc Binding Sites List in 5sj8
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:42.5
occ:1.00
 OD2 A:ASP564 2.0 39.5 1.0
OD1 A:ASP674 2.1 42.5 1.0
NE2 A:HIS529 2.2 37.3 1.0
NE2 A:HIS563 2.2 34.3 1.0
O A:HOH939 2.3 37.7 1.0
CG A:ASP674 2.9 41.6 1.0
CG A:ASP564 3.1 41.1 1.0
CD2 A:HIS563 3.1 35.1 1.0
CE1 A:HIS529 3.1 35.6 1.0
CD2 A:HIS529 3.1 38.2 1.0
OD2 A:ASP674 3.2 47.1 1.0
CE1 A:HIS563 3.2 37.4 1.0
OD1 A:ASP564 3.6 38.5 1.0
MG A:MG802 3.9 36.7 1.0
CD2 A:HIS525 4.1 42.1 1.0
CG A:HIS563 4.2 36.8 1.0
ND1 A:HIS529 4.2 33.9 1.0
CB A:ASP564 4.3 38.8 1.0
ND1 A:HIS563 4.3 35.0 1.0
CG A:HIS529 4.3 34.6 1.0
CB A:ASP674 4.3 43.5 1.0
O A:HOH924 4.4 36.3 1.0
O A:HOH963 4.4 36.1 1.0
NE2 A:HIS525 4.4 42.7 1.0
O A:HOH918 4.6 36.1 1.0
O A:ASP674 4.7 45.2 1.0
CG2 A:VAL533 4.8 33.9 1.0
CA A:ASP674 4.8 41.8 1.0

Zinc binding site 2 out of 4 in 5sj8

Go back to Zinc Binding Sites List in 5sj8
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:38.7
occ:1.00
 NE2 B:HIS563 2.0 31.3 1.0
NE2 B:HIS529 2.1 37.5 1.0
OD1 B:ASP674 2.1 33.9 1.0
OD2 B:ASP564 2.1 30.5 1.0
O B:HOH938 2.2 22.5 1.0
O B:HOH955 2.3 39.2 1.0
CD2 B:HIS563 3.0 31.4 1.0
CE1 B:HIS563 3.0 35.2 1.0
CD2 B:HIS529 3.0 39.8 1.0
CE1 B:HIS529 3.1 40.0 1.0
CG B:ASP564 3.1 33.8 1.0
CG B:ASP674 3.1 38.4 1.0
OD2 B:ASP674 3.4 42.1 1.0
OD1 B:ASP564 3.6 33.9 1.0
MG B:MG802 3.9 31.5 1.0
ND1 B:HIS563 4.1 31.1 1.0
CG B:HIS563 4.1 33.3 1.0
O B:HOH971 4.1 31.8 1.0
ND1 B:HIS529 4.2 38.3 1.0
CG B:HIS529 4.2 34.9 1.0
CD2 B:HIS525 4.2 35.7 1.0
CB B:ASP564 4.3 31.5 1.0
O B:HOH923 4.4 41.6 1.0
CB B:ASP674 4.5 38.3 1.0
NE2 B:HIS525 4.5 34.6 1.0
O B:HOH915 4.6 30.5 1.0
CG2 B:VAL533 4.7 30.3 1.0
O B:ASP674 4.7 34.6 1.0
CA B:ASP674 4.8 38.4 1.0

Zinc binding site 3 out of 4 in 5sj8

Go back to Zinc Binding Sites List in 5sj8
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:42.9
occ:1.00
 O C:HOH941 2.0 45.8 1.0
OD2 C:ASP564 2.0 40.1 1.0
OD1 C:ASP674 2.1 37.4 1.0
NE2 C:HIS529 2.1 37.2 1.0
NE2 C:HIS563 2.2 38.7 1.0
O C:HOH914 2.3 33.6 1.0
CG C:ASP674 2.9 35.3 1.0
CG C:ASP564 3.1 37.5 1.0
CE1 C:HIS529 3.1 41.8 1.0
CD2 C:HIS529 3.1 38.7 1.0
CD2 C:HIS563 3.1 35.8 1.0
OD2 C:ASP674 3.1 34.2 1.0
CE1 C:HIS563 3.3 37.2 1.0
OD1 C:ASP564 3.6 35.7 1.0
MG C:MG802 3.9 32.2 1.0
CD2 C:HIS525 4.1 39.7 1.0
ND1 C:HIS529 4.2 38.9 1.0
O C:HOH968 4.2 33.9 1.0
CG C:HIS529 4.2 39.4 1.0
CG C:HIS563 4.3 37.6 1.0
CB C:ASP564 4.3 31.6 1.0
ND1 C:HIS563 4.3 33.9 1.0
CB C:ASP674 4.3 35.7 1.0
O C:HOH933 4.3 43.8 1.0
NE2 C:HIS525 4.4 36.4 1.0
O C:HOH916 4.7 30.9 1.0
O C:ASP674 4.7 45.2 1.0
CA C:ASP674 4.7 36.7 1.0
CG2 C:VAL533 4.9 32.8 1.0

Zinc binding site 4 out of 4 in 5sj8

Go back to Zinc Binding Sites List in 5sj8
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile


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 12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaene-7-Carbonitrile within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:51.4
occ:1.00
 NE2 D:HIS563 2.0 38.5 1.0
OD2 D:ASP564 2.1 52.9 1.0
OD1 D:ASP674 2.1 51.8 1.0
O D:HOH926 2.2 39.1 1.0
O D:HOH909 2.2 40.8 1.0
NE2 D:HIS529 2.3 49.1 1.0
CD2 D:HIS563 2.9 36.1 1.0
CG D:ASP674 3.0 46.4 1.0
CE1 D:HIS563 3.1 43.0 1.0
CG D:ASP564 3.1 45.4 1.0
CD2 D:HIS529 3.2 46.5 1.0
OD2 D:ASP674 3.2 47.0 1.0
CE1 D:HIS529 3.3 48.6 1.0
OD1 D:ASP564 3.6 42.1 1.0
MG D:MG802 3.8 48.6 1.0
O D:HOH916 4.0 40.1 1.0
CG D:HIS563 4.1 37.1 1.0
ND1 D:HIS563 4.2 42.6 1.0
CB D:ASP564 4.3 41.7 1.0
CD2 D:HIS525 4.3 53.7 1.0
CG D:HIS529 4.4 47.3 1.0
CB D:ASP674 4.4 51.0 1.0
ND1 D:HIS529 4.4 49.0 1.0
O D:HOH906 4.5 38.3 1.0
O D:ASP674 4.6 46.5 1.0
NE2 D:HIS525 4.6 49.9 1.0
CG2 D:VAL533 4.8 44.2 1.0
CA D:ASP674 4.8 46.8 1.0
O D:HOH903 5.0 41.4 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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