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Zinc in PDB 5shk: Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine, PDB code: 5shk was solved by C.Joseph, J.Benz, A.Flohr, G.Jaeschke, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.84 / 2.00
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.736, 134.736, 235.207, 90, 90, 120
R / Rfree (%) 18.9 / 21.8

Other elements in 5shk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine 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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine (pdb code 5shk). 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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine, PDB code: 5shk:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 5shk

Go back to Zinc Binding Sites List in 5shk
Zinc binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine


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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn801

b:29.5
occ:1.00
 NE2 A:HIS563 2.1 23.9 1.0
OD2 A:ASP564 2.1 25.2 1.0
O A:HOH959 2.1 26.0 1.0
NE2 A:HIS529 2.1 26.0 1.0
OD1 A:ASP674 2.2 28.5 1.0
O A:HOH1002 2.2 30.6 1.0
CD2 A:HIS563 3.0 24.7 1.0
CG A:ASP674 3.1 27.9 1.0
CG A:ASP564 3.1 25.8 1.0
CD2 A:HIS529 3.1 25.2 1.0
CE1 A:HIS563 3.1 25.4 1.0
CE1 A:HIS529 3.2 26.3 1.0
OD2 A:ASP674 3.3 31.8 1.0
OD1 A:ASP564 3.6 24.1 1.0
MG A:MG802 3.8 24.0 1.0
O A:HOH1007 4.0 23.9 1.0
O A:HOH990 4.1 34.1 1.0
CG A:HIS563 4.1 25.0 1.0
ND1 A:HIS563 4.2 24.5 1.0
CD2 A:HIS525 4.2 27.7 1.0
CG A:HIS529 4.2 26.0 1.0
ND1 A:HIS529 4.3 25.1 1.0
CB A:ASP564 4.3 24.7 1.0
CB A:ASP674 4.4 26.3 1.0
NE2 A:HIS525 4.6 27.9 1.0
O A:HOH947 4.6 21.7 1.0
CG2 A:VAL533 4.7 22.9 1.0
O A:ASP674 4.8 26.2 1.0
CA A:ASP674 4.8 25.4 1.0

Zinc binding site 2 out of 4 in 5shk

Go back to Zinc Binding Sites List in 5shk
Zinc binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine


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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn801

b:28.9
occ:1.00
 O B:HOH914 2.0 19.4 1.0
NE2 B:HIS563 2.1 24.5 1.0
OD2 B:ASP564 2.1 25.7 1.0
OD1 B:ASP674 2.2 24.4 1.0
NE2 B:HIS529 2.2 24.8 1.0
O B:HOH972 2.2 35.5 1.0
CG B:ASP674 3.0 24.6 1.0
CD2 B:HIS563 3.0 24.0 1.0
CE1 B:HIS563 3.1 25.0 1.0
CG B:ASP564 3.1 24.4 1.0
CD2 B:HIS529 3.2 24.7 1.0
CE1 B:HIS529 3.2 26.5 1.0
OD2 B:ASP674 3.2 25.0 1.0
OD1 B:ASP564 3.6 24.3 1.0
MG B:MG802 3.7 21.0 1.0
O B:HOH961 4.0 37.2 1.0
O B:HOH1009 4.0 21.1 1.0
CD2 B:HIS525 4.1 28.2 1.0
CG B:HIS563 4.2 24.4 1.0
ND1 B:HIS563 4.2 24.1 1.0
ND1 B:HIS529 4.3 24.7 1.0
CB B:ASP564 4.3 23.7 1.0
CG B:HIS529 4.3 24.9 1.0
NE2 B:HIS525 4.4 28.5 1.0
CB B:ASP674 4.4 23.2 1.0
O B:HOH924 4.6 22.8 1.0
CG2 B:VAL533 4.7 25.4 1.0
O B:ASP674 4.8 24.9 1.0
CA B:ASP674 4.8 24.4 1.0

Zinc binding site 3 out of 4 in 5shk

Go back to Zinc Binding Sites List in 5shk
Zinc binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine


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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn801

b:31.1
occ:1.00
 O C:HOH914 2.0 19.7 1.0
OD2 C:ASP564 2.1 26.0 1.0
NE2 C:HIS529 2.1 26.3 1.0
NE2 C:HIS563 2.1 25.4 1.0
O C:HOH976 2.1 37.1 1.0
OD1 C:ASP674 2.2 28.6 1.0
CD2 C:HIS563 3.0 24.9 1.0
CG C:ASP674 3.0 29.0 1.0
CE1 C:HIS529 3.1 28.6 1.0
CG C:ASP564 3.1 25.2 1.0
CD2 C:HIS529 3.1 27.4 1.0
CE1 C:HIS563 3.2 25.1 1.0
OD2 C:ASP674 3.2 30.7 1.0
OD1 C:ASP564 3.6 26.4 1.0
MG C:MG802 3.8 26.4 1.0
O C:HOH1004 4.0 28.7 1.0
CD2 C:HIS525 4.1 32.5 1.0
O C:HOH974 4.2 43.3 1.0
CG C:HIS563 4.2 24.1 1.0
ND1 C:HIS529 4.2 27.9 1.0
CB C:ASP564 4.2 23.6 1.0
CG C:HIS529 4.2 27.8 1.0
ND1 C:HIS563 4.2 24.8 1.0
CB C:ASP674 4.4 28.7 1.0
NE2 C:HIS525 4.5 32.8 1.0
O C:HOH931 4.6 26.3 1.0
CG2 C:VAL533 4.7 27.1 1.0
CA C:ASP674 4.8 28.5 1.0
O C:ASP674 4.8 29.8 1.0

Zinc binding site 4 out of 4 in 5shk

Go back to Zinc Binding Sites List in 5shk
Zinc binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine


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-(6- Methylpyridin-2-Yl)-5-Pyridin-3-Yl-1,7-Naphthyridin-8-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn801

b:40.5
occ:1.00
 O D:HOH917 2.1 30.2 1.0
NE2 D:HIS529 2.1 41.0 1.0
NE2 D:HIS563 2.2 29.4 1.0
OD2 D:ASP564 2.2 37.5 1.0
OD1 D:ASP674 2.3 34.8 1.0
O D:HOH951 2.3 34.1 1.0
CD2 D:HIS563 3.0 30.9 1.0
CD2 D:HIS529 3.1 40.0 1.0
CG D:ASP674 3.1 37.4 1.0
CG D:ASP564 3.1 35.8 1.0
CE1 D:HIS529 3.2 41.9 1.0
CE1 D:HIS563 3.2 30.9 1.0
OD2 D:ASP674 3.3 34.8 1.0
OD1 D:ASP564 3.6 35.4 1.0
MG D:MG802 3.9 36.6 1.0
O D:HOH964 4.0 38.7 1.0
CD2 D:HIS525 4.2 42.4 1.0
O D:HOH948 4.2 46.5 1.0
CG D:HIS563 4.2 30.2 1.0
CG D:HIS529 4.3 38.5 1.0
ND1 D:HIS529 4.3 38.6 1.0
CB D:ASP564 4.3 35.3 1.0
ND1 D:HIS563 4.3 30.1 1.0
O D:HOH920 4.5 35.1 1.0
CB D:ASP674 4.5 35.1 1.0
NE2 D:HIS525 4.6 44.9 1.0
CG2 D:VAL533 4.7 36.4 1.0
O D:ASP674 4.8 34.5 1.0
CA D:ASP674 4.9 35.9 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 05:31:00 2024

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