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Magnesium 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:

Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 4 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5shk

Go back to Magnesium Binding Sites List in 5shk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:24.0
occ:1.00
 O A:HOH1007 1.9 23.9 1.0
O A:HOH959 2.0 26.0 1.0
OD1 A:ASP564 2.0 24.1 1.0
O A:HOH947 2.0 21.7 1.0
O A:HOH960 2.0 23.0 1.0
O A:HOH926 2.1 25.7 1.0
CG A:ASP564 3.1 25.8 1.0
OD2 A:ASP564 3.4 25.2 1.0
ZN A:ZN801 3.8 29.5 1.0
O A:HOH1002 4.0 30.6 1.0
OE2 A:GLU592 4.0 31.7 1.0
NE2 A:HIS595 4.1 27.7 1.0
OG1 A:THR633 4.3 28.2 1.0
CD2 A:HIS563 4.3 24.7 1.0
CD2 A:HIS567 4.3 29.7 1.0
O A:HOH992 4.3 31.0 1.0
CD2 A:HIS595 4.3 25.7 1.0
O A:HIS563 4.3 26.6 1.0
CB A:ASP564 4.4 24.7 1.0
OD2 A:ASP674 4.5 31.8 1.0
O A:THR633 4.5 28.0 1.0
NE2 A:HIS567 4.5 28.6 1.0
NE2 A:HIS563 4.6 23.9 1.0
CD2 A:HIS525 4.7 27.7 1.0
CB A:THR633 4.7 27.6 1.0
CA A:ASP564 4.8 24.7 1.0
NE2 A:HIS525 4.8 27.9 1.0
CD A:GLU592 4.8 30.3 1.0
CG A:GLU592 4.8 29.0 1.0

Magnesium binding site 2 out of 4 in 5shk

Go back to Magnesium Binding Sites List in 5shk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:21.0
occ:1.00
 O B:HOH924 1.9 22.8 1.0
O B:HOH914 2.0 19.4 1.0
O B:HOH1009 2.0 21.1 1.0
OD1 B:ASP564 2.0 24.3 1.0
O B:HOH921 2.1 19.8 1.0
O B:HOH978 2.1 18.8 1.0
CG B:ASP564 3.1 24.4 1.0
OD2 B:ASP564 3.4 25.7 1.0
ZN B:ZN801 3.7 28.9 1.0
O B:HOH972 4.0 35.5 1.0
OE2 B:GLU592 4.0 29.0 1.0
NE2 B:HIS595 4.1 26.8 1.0
CD2 B:HIS563 4.1 24.0 1.0
OG1 B:THR633 4.2 23.3 1.0
O B:HOH996 4.3 28.4 1.0
CD2 B:HIS567 4.3 22.5 1.0
OD2 B:ASP674 4.3 25.0 1.0
CD2 B:HIS595 4.3 26.6 1.0
O B:HIS563 4.3 25.8 1.0
CB B:ASP564 4.4 23.7 1.0
NE2 B:HIS567 4.4 23.4 1.0
NE2 B:HIS563 4.4 24.5 1.0
O B:THR633 4.5 25.9 1.0
CD2 B:HIS525 4.6 28.2 1.0
CB B:THR633 4.6 25.3 1.0
NE2 B:HIS525 4.7 28.5 1.0
CA B:ASP564 4.7 24.4 1.0
CG B:GLU592 4.8 26.0 1.0
CD B:GLU592 4.9 25.8 1.0

Magnesium binding site 3 out of 4 in 5shk

Go back to Magnesium Binding Sites List in 5shk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:26.4
occ:1.00
 O C:HOH1004 2.0 28.7 1.0
OD1 C:ASP564 2.0 26.4 1.0
O C:HOH970 2.0 27.0 1.0
O C:HOH914 2.1 19.7 1.0
O C:HOH931 2.1 26.3 1.0
O C:HOH933 2.2 24.4 1.0
CG C:ASP564 3.0 25.2 1.0
OD2 C:ASP564 3.4 26.0 1.0
ZN C:ZN801 3.8 31.1 1.0
O C:HOH976 3.9 37.1 1.0
NE2 C:HIS595 4.0 27.1 1.0
OE2 C:GLU592 4.0 32.3 1.0
CD2 C:HIS567 4.2 31.5 1.0
CD2 C:HIS563 4.2 24.9 1.0
OG1 C:THR633 4.2 30.9 1.0
O C:HIS563 4.3 26.8 1.0
OD2 C:ASP674 4.3 30.7 1.0
O C:HOH972 4.3 35.5 1.0
CD2 C:HIS595 4.3 26.1 1.0
NE2 C:HIS567 4.4 31.6 1.0
CB C:ASP564 4.4 23.6 1.0
O C:THR633 4.5 31.0 1.0
NE2 C:HIS563 4.6 25.4 1.0
CB C:THR633 4.6 28.3 1.0
CA C:ASP564 4.7 24.9 1.0
CG C:GLU592 4.7 28.2 1.0
CD2 C:HIS525 4.8 32.5 1.0
CD C:GLU592 4.8 30.4 1.0
NE2 C:HIS525 4.9 32.8 1.0

Magnesium binding site 4 out of 4 in 5shk

Go back to Magnesium Binding Sites List in 5shk
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg802

b:36.6
occ:1.00
 O D:HOH920 2.1 35.1 1.0
O D:HOH959 2.1 26.1 1.0
O D:HOH964 2.1 38.7 1.0
O D:HOH916 2.1 35.0 1.0
O D:HOH917 2.1 30.2 1.0
OD1 D:ASP564 2.2 35.4 1.0
CG D:ASP564 3.2 35.8 1.0
OD2 D:ASP564 3.5 37.5 1.0
ZN D:ZN801 3.9 40.5 1.0
OE2 D:GLU592 3.9 40.9 1.0
O D:HOH962 4.0 37.4 1.0
O D:HOH951 4.1 34.1 1.0
NE2 D:HIS595 4.1 38.4 1.0
OG1 D:THR633 4.2 36.8 1.0
CD2 D:HIS567 4.2 44.6 1.0
CD2 D:HIS595 4.3 37.2 1.0
CD2 D:HIS563 4.4 30.9 1.0
OD2 D:ASP674 4.4 34.8 1.0
O D:HIS563 4.4 35.1 1.0
NE2 D:HIS567 4.4 43.0 1.0
O D:THR633 4.5 38.1 1.0
CB D:ASP564 4.5 35.3 1.0
CB D:THR633 4.7 38.4 1.0
CD2 D:HIS525 4.7 42.4 1.0
CD D:GLU592 4.8 38.5 1.0
NE2 D:HIS563 4.8 29.4 1.0
CG D:GLU592 4.8 39.0 1.0
NE2 D:HIS525 4.8 44.9 1.0
CA D:ASP564 4.9 34.9 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 Sep 30 04:00:19 2024

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