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

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One, PDB code: 5sgz was solved by C.Joseph, J.Benz, A.Flohr, K.Groebke-Zbinden, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.42 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.979, 134.979, 235.207, 90, 90, 120
R / Rfree (%) 18.8 / 22.3

Other elements in 5sgz:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One (pdb code 5sgz). 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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One, PDB code: 5sgz:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5sgz

Go back to Zinc Binding Sites List in 5sgz
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:34.0
occ:1.00
 OD2 A:ASP564 2.0 26.4 1.0
OD1 A:ASP674 2.1 36.0 1.0
NE2 A:HIS563 2.1 28.8 1.0
NE2 A:HIS529 2.1 29.2 1.0
O A:HOH911 2.2 32.3 1.0
O A:HOH955 2.3 36.5 1.0
CD2 A:HIS563 3.0 26.7 1.0
CG A:ASP674 3.0 36.3 1.0
CD2 A:HIS529 3.1 28.4 1.0
CG A:ASP564 3.1 28.6 1.0
CE1 A:HIS563 3.1 27.1 1.0
CE1 A:HIS529 3.2 30.6 1.0
OD2 A:ASP674 3.3 28.8 1.0
OD1 A:ASP564 3.7 30.3 1.0
MG A:MG802 3.8 27.2 1.0
O A:HOH987 4.0 28.0 1.0
CD2 A:HIS525 4.1 34.2 1.0
CG A:HIS563 4.1 28.1 1.0
ND1 A:HIS563 4.2 28.3 1.0
O A:HOH953 4.2 28.2 1.0
CB A:ASP564 4.2 26.4 1.0
CG A:HIS529 4.3 26.1 1.0
ND1 A:HIS529 4.3 26.7 1.0
CB A:ASP674 4.4 30.7 1.0
NE2 A:HIS525 4.4 32.3 1.0
O A:HOH943 4.7 29.3 1.0
CG2 A:VAL533 4.7 34.3 1.0
O A:ASP674 4.8 32.9 1.0
CA A:ASP674 4.9 31.0 1.0

Zinc binding site 2 out of 4 in 5sgz

Go back to Zinc Binding Sites List in 5sgz
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:34.0
occ:1.00
 O B:HOH915 2.0 30.5 1.0
NE2 B:HIS563 2.1 24.3 1.0
OD2 B:ASP564 2.1 28.7 1.0
OD1 B:ASP674 2.2 35.5 1.0
NE2 B:HIS529 2.2 27.7 1.0
O B:HOH977 2.4 34.4 1.0
CE1 B:HIS563 3.0 28.9 1.0
CG B:ASP564 3.0 32.5 1.0
CG B:ASP674 3.0 32.8 1.0
CD2 B:HIS563 3.1 26.5 1.0
CD2 B:HIS529 3.1 27.1 1.0
CE1 B:HIS529 3.3 30.5 1.0
OD2 B:ASP674 3.3 38.3 1.0
OD1 B:ASP564 3.5 29.6 1.0
MG B:MG802 3.9 31.3 1.0
O B:HOH974 4.0 28.9 1.0
CD2 B:HIS525 4.1 36.1 1.0
ND1 B:HIS563 4.1 28.2 1.0
O B:HOH954 4.2 26.7 1.0
CG B:HIS563 4.2 28.3 1.0
CB B:ASP564 4.2 30.6 1.0
CG B:HIS529 4.3 29.4 1.0
ND1 B:HIS529 4.3 29.4 1.0
CB B:ASP674 4.4 33.8 1.0
NE2 B:HIS525 4.4 34.5 1.0
O B:HOH912 4.6 28.7 1.0
O B:ASP674 4.8 33.8 1.0
CA B:ASP674 4.8 31.9 1.0
CG2 B:VAL533 4.8 31.8 1.0

Zinc binding site 3 out of 4 in 5sgz

Go back to Zinc Binding Sites List in 5sgz
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:35.5
occ:1.00
 O C:HOH917 2.0 31.3 1.0
NE2 C:HIS563 2.1 31.6 1.0
OD2 C:ASP564 2.1 29.7 1.0
OD1 C:ASP674 2.1 32.5 1.0
NE2 C:HIS529 2.2 40.2 1.0
O C:HOH979 2.2 32.1 1.0
CG C:ASP674 2.9 34.8 1.0
CD2 C:HIS563 2.9 28.5 1.0
OD2 C:ASP674 3.0 36.4 1.0
CG C:ASP564 3.1 31.1 1.0
CD2 C:HIS529 3.2 36.7 1.0
CE1 C:HIS563 3.2 30.6 1.0
CE1 C:HIS529 3.2 37.3 1.0
OD1 C:ASP564 3.6 30.1 1.0
MG C:MG802 3.8 27.2 1.0
CG C:HIS563 4.1 29.6 1.0
O C:HOH994 4.1 31.4 1.0
CD2 C:HIS525 4.2 35.6 1.0
O C:HOH952 4.2 39.8 1.0
ND1 C:HIS563 4.2 27.9 1.0
CB C:ASP564 4.2 31.7 1.0
ND1 C:HIS529 4.3 35.9 1.0
CG C:HIS529 4.3 30.6 1.0
CB C:ASP674 4.3 35.7 1.0
NE2 C:HIS525 4.5 33.4 1.0
O C:HOH931 4.7 29.2 1.0
CA C:ASP674 4.7 32.7 1.0
CG2 C:VAL533 4.8 29.9 1.0
O C:ASP674 4.8 36.2 1.0

Zinc binding site 4 out of 4 in 5sgz

Go back to Zinc Binding Sites List in 5sgz
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 3-(2- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-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- Chlorophenyl)-12-Methoxy-5-Methyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,9,11-Pentaen-7-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:43.8
occ:1.00
 O D:HOH913 2.0 37.5 1.0
OD2 D:ASP564 2.1 36.1 1.0
NE2 D:HIS563 2.1 34.3 1.0
NE2 D:HIS529 2.2 40.2 1.0
OD1 D:ASP674 2.2 43.5 1.0
O D:HOH958 2.3 39.0 1.0
CD2 D:HIS563 2.9 34.8 1.0
CG D:ASP564 3.1 35.0 1.0
CG D:ASP674 3.1 41.0 1.0
CD2 D:HIS529 3.1 44.9 1.0
CE1 D:HIS529 3.2 41.0 1.0
CE1 D:HIS563 3.3 36.5 1.0
OD2 D:ASP674 3.3 40.5 1.0
OD1 D:ASP564 3.6 40.0 1.0
MG D:MG802 3.9 36.8 1.0
CG D:HIS563 4.1 37.5 1.0
CB D:ASP564 4.1 35.4 1.0
O D:HOH960 4.2 33.5 1.0
CD2 D:HIS525 4.3 48.6 1.0
CG D:HIS529 4.3 39.0 1.0
ND1 D:HIS563 4.3 33.7 1.0
ND1 D:HIS529 4.3 42.5 1.0
O D:HOH920 4.3 48.5 1.0
CB D:ASP674 4.4 43.2 1.0
O D:HOH914 4.5 42.4 1.0
NE2 D:HIS525 4.6 47.5 1.0
CG2 D:VAL533 4.7 38.5 1.0
O D:ASP674 4.8 38.4 1.0
CA D:ASP674 4.8 40.1 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 05:22:59 2024

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