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Zinc in PDB 5si5: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide

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

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

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5 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) 43.35 / 2.27
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.764, 134.764, 234.884, 90, 90, 120
R / Rfree (%) 18 / 22.4

Other elements in 5si5:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide 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 N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide (pdb code 5si5). 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 N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide, PDB code: 5si5:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5si5

Go back to Zinc Binding Sites List in 5si5
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:34.0
occ:1.00
 OD2 A:ASP564 2.1 28.2 1.0
NE2 A:HIS529 2.1 28.6 1.0
OD1 A:ASP674 2.1 33.6 1.0
NE2 A:HIS563 2.1 28.1 1.0
O A:HOH953 2.2 32.5 1.0
O A:HOH970 2.3 27.9 1.0
CD2 A:HIS563 3.0 28.5 1.0
CG A:ASP674 3.0 31.8 1.0
CD2 A:HIS529 3.1 28.7 1.0
CE1 A:HIS529 3.1 29.8 1.0
CG A:ASP564 3.1 30.0 1.0
CE1 A:HIS563 3.2 30.5 1.0
OD2 A:ASP674 3.3 32.6 1.0
OD1 A:ASP564 3.7 27.6 1.0
MG A:MG802 3.9 30.8 1.0
CD2 A:HIS525 4.2 30.9 1.0
CG A:HIS563 4.2 29.5 1.0
ND1 A:HIS529 4.2 27.4 1.0
CG A:HIS529 4.2 27.6 1.0
ND1 A:HIS563 4.2 28.9 1.0
CB A:ASP564 4.3 28.4 1.0
O A:HOH990 4.3 26.7 1.0
CB A:ASP674 4.4 31.0 1.0
O A:HOH963 4.4 32.4 1.0
NE2 A:HIS525 4.4 30.6 1.0
O A:HOH930 4.6 26.2 1.0
O A:ASP674 4.7 29.2 1.0
CG2 A:VAL533 4.7 25.8 1.0
CA A:ASP674 4.8 28.4 1.0

Zinc binding site 2 out of 4 in 5si5

Go back to Zinc Binding Sites List in 5si5
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:32.5
occ:1.00
 O B:HOH931 2.1 22.9 1.0
OD2 B:ASP564 2.1 29.4 1.0
NE2 B:HIS563 2.1 25.3 1.0
OD1 B:ASP674 2.1 32.7 1.0
NE2 B:HIS529 2.1 26.4 1.0
O B:HOH953 2.5 36.3 1.0
CD2 B:HIS563 2.9 27.5 1.0
CG B:ASP564 3.0 29.8 1.0
CG B:ASP674 3.1 29.8 1.0
CD2 B:HIS529 3.1 26.8 1.0
CE1 B:HIS529 3.2 29.7 1.0
CE1 B:HIS563 3.2 28.7 1.0
OD2 B:ASP674 3.3 31.5 1.0
OD1 B:ASP564 3.5 26.5 1.0
MG B:MG802 3.8 23.1 1.0
O B:HOH987 4.1 17.9 1.0
CG B:HIS563 4.1 25.5 1.0
CD2 B:HIS525 4.2 27.7 1.0
ND1 B:HIS563 4.2 24.6 1.0
CB B:ASP564 4.2 29.8 1.0
CG B:HIS529 4.3 26.7 1.0
ND1 B:HIS529 4.3 27.2 1.0
CB B:ASP674 4.4 30.1 1.0
NE2 B:HIS525 4.4 29.8 1.0
O B:HOH940 4.5 29.6 1.0
O B:HOH934 4.6 29.3 1.0
CG2 B:VAL533 4.7 30.9 1.0
O B:ASP674 4.8 30.9 1.0
CA B:ASP674 4.8 29.1 1.0

Zinc binding site 3 out of 4 in 5si5

Go back to Zinc Binding Sites List in 5si5
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:35.1
occ:1.00
 OD2 C:ASP564 2.1 29.6 1.0
NE2 C:HIS529 2.1 29.3 1.0
O C:HOH920 2.1 22.3 1.0
OD1 C:ASP674 2.1 30.5 1.0
NE2 C:HIS563 2.2 30.4 1.0
O C:HOH960 2.3 37.9 1.0
CG C:ASP674 3.0 29.4 1.0
CE1 C:HIS529 3.1 29.7 1.0
CD2 C:HIS563 3.1 28.9 1.0
CD2 C:HIS529 3.1 28.7 1.0
CG C:ASP564 3.2 31.2 1.0
OD2 C:ASP674 3.2 32.5 1.0
CE1 C:HIS563 3.2 30.2 1.0
OD1 C:ASP564 3.7 30.4 1.0
MG C:MG802 3.8 28.0 1.0
CD2 C:HIS525 4.1 34.5 1.0
ND1 C:HIS529 4.2 25.8 1.0
CG C:HIS529 4.2 28.8 1.0
O C:HOH989 4.2 24.6 1.0
CG C:HIS563 4.3 29.2 1.0
ND1 C:HIS563 4.3 29.9 1.0
CB C:ASP564 4.3 29.9 1.0
CB C:ASP674 4.4 28.9 1.0
O C:HOH955 4.4 33.5 1.0
NE2 C:HIS525 4.4 34.4 1.0
O C:HOH979 4.6 47.5 1.0
O C:HOH919 4.6 29.6 1.0
O C:ASP674 4.7 30.5 1.0
CG2 C:VAL533 4.7 29.2 1.0
CA C:ASP674 4.8 30.3 1.0

Zinc binding site 4 out of 4 in 5si5

Go back to Zinc Binding Sites List in 5si5
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(12- Methoxy-5-Methyl-3-Propyl-2,4,8,13-Tetrazatricyclo[7.4.0.02, 6]Trideca-1(13),3,5,7,9,11-Hexaen-7-Yl)Methanesulfonamide


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

b:48.1
occ:1.00
 NE2 D:HIS563 2.0 32.7 1.0
O D:HOH918 2.1 36.8 1.0
OD1 D:ASP674 2.2 39.9 1.0
NE2 D:HIS529 2.2 39.1 1.0
OD2 D:ASP564 2.3 45.8 1.0
O D:HOH935 2.3 44.3 1.0
CD2 D:HIS563 2.9 35.9 1.0
CG D:ASP674 3.1 44.1 1.0
CE1 D:HIS563 3.1 34.6 1.0
CG D:ASP564 3.2 41.8 1.0
CE1 D:HIS529 3.2 40.7 1.0
CD2 D:HIS529 3.2 41.1 1.0
OD2 D:ASP674 3.3 42.8 1.0
OD1 D:ASP564 3.6 39.3 1.0
MG D:MG802 3.8 48.6 1.0
CG D:HIS563 4.1 35.2 1.0
ND1 D:HIS563 4.2 34.7 1.0
O D:HOH938 4.2 36.6 1.0
CD2 D:HIS525 4.3 51.8 1.0
CB D:ASP564 4.3 40.3 1.0
ND1 D:HIS529 4.3 42.9 1.0
CG D:HIS529 4.3 38.6 1.0
CB D:ASP674 4.4 46.2 1.0
O D:HOH925 4.4 44.8 1.0
O D:ASP674 4.6 45.0 1.0
NE2 D:HIS525 4.6 48.4 1.0
O D:HOH911 4.7 36.8 1.0
CG2 D:VAL533 4.8 50.3 1.0
CA D:ASP674 4.8 47.8 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 05:41:13 2024

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