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Magnesium in PDB 5sjk: Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One, PDB code: 5sjk was solved by C.Joseph, J.Benz, A.Flohr, E.Kyburz, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.38 / 2.24
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.878, 134.878, 234.027, 90, 90, 120
R / Rfree (%) 18.3 / 23.5

Other elements in 5sjk:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One also contains other interesting chemical elements:

Chlorine (Cl) 8 atoms
Zinc (Zn) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One (pdb code 5sjk). 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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One, PDB code: 5sjk:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5sjk

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One


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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.5
occ:1.00
 O A:HOH1002 2.0 31.2 1.0
OD1 A:ASP564 2.0 26.2 1.0
O A:HOH934 2.0 26.4 1.0
O A:HOH956 2.1 26.6 1.0
O A:HOH954 2.1 28.0 1.0
O A:HOH912 2.2 27.6 1.0
CG A:ASP564 3.1 29.2 1.0
OD2 A:ASP564 3.4 30.9 1.0
OE2 A:GLU592 3.9 34.2 1.0
ZN A:ZN801 3.9 35.8 1.0
NE2 A:HIS595 4.0 26.7 1.0
CD2 A:HIS567 4.1 33.1 1.0
O A:HOH969 4.2 33.3 1.0
O A:HOH987 4.2 43.9 1.0
CD2 A:HIS595 4.3 27.2 1.0
OG1 A:THR633 4.3 31.1 1.0
O A:HOH950 4.3 36.2 1.0
NE2 A:HIS567 4.3 33.5 1.0
O A:HIS563 4.4 29.8 1.0
CD2 A:HIS563 4.4 26.3 1.0
CB A:ASP564 4.4 27.9 1.0
O A:THR633 4.5 32.6 1.0
OD2 A:ASP674 4.6 39.4 1.0
CG A:GLU592 4.7 33.2 1.0
NE2 A:HIS563 4.7 27.6 1.0
CD A:GLU592 4.7 35.8 1.0
CD2 A:HIS525 4.8 28.3 1.0
CA A:ASP564 4.8 28.9 1.0
CB A:THR633 4.8 29.2 1.0
NE2 A:HIS525 4.9 28.5 1.0

Magnesium binding site 2 out of 4 in 5sjk

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Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One


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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:24.0
occ:1.00
 O B:HOH950 1.9 21.3 1.0
O B:HOH943 1.9 25.4 1.0
OD1 B:ASP564 2.0 27.8 1.0
O B:HOH1009 2.1 21.3 1.0
O B:HOH944 2.1 26.1 1.0
O B:HOH927 2.2 17.5 1.0
CG B:ASP564 3.1 28.7 1.0
OD2 B:ASP564 3.4 27.6 1.0
ZN B:ZN801 3.8 33.7 1.0
NE2 B:HIS595 3.9 34.0 1.0
O B:HOH980 4.0 34.6 1.0
CD2 B:HIS563 4.1 25.7 1.0
OE2 B:GLU592 4.2 26.4 1.0
OG1 B:THR633 4.2 31.8 1.0
O B:HIS563 4.2 33.2 1.0
CD2 B:HIS595 4.2 38.6 1.0
O B:HOH955 4.3 31.4 1.0
CD2 B:HIS567 4.3 30.3 1.0
OD2 B:ASP674 4.4 32.9 1.0
CB B:ASP564 4.4 28.4 1.0
NE2 B:HIS563 4.5 26.9 1.0
NE2 B:HIS567 4.5 31.0 1.0
O B:THR633 4.6 28.6 1.0
CD2 B:HIS525 4.7 31.6 1.0
CB B:THR633 4.7 31.4 1.0
CA B:ASP564 4.7 29.7 1.0
CG B:GLU592 4.8 30.6 1.0
CD B:GLU592 4.9 30.3 1.0
NE2 B:HIS525 4.9 31.3 1.0

Magnesium binding site 3 out of 4 in 5sjk

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Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One


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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:29.9
occ:1.00
 O C:HOH941 2.0 29.8 1.0
O C:HOH929 2.0 25.4 1.0
O C:HOH964 2.0 31.8 1.0
O C:HOH1006 2.1 29.4 1.0
OD1 C:ASP564 2.1 29.9 1.0
O C:HOH940 2.1 19.9 1.0
CG C:ASP564 3.0 31.7 1.0
OD2 C:ASP564 3.3 30.8 1.0
ZN C:ZN801 3.7 34.3 1.0
O C:HOH981 3.9 40.3 1.0
OE2 C:GLU592 4.0 32.1 1.0
NE2 C:HIS595 4.1 36.0 1.0
CD2 C:HIS567 4.1 32.1 1.0
O C:HOH958 4.2 33.6 1.0
CD2 C:HIS563 4.2 28.3 1.0
O C:HOH1019 4.3 53.6 1.0
OD2 C:ASP674 4.3 25.9 1.0
OG1 C:THR633 4.3 31.8 1.0
NE2 C:HIS567 4.3 32.8 1.0
CD2 C:HIS595 4.4 34.5 1.0
O C:HIS563 4.4 28.3 1.0
CB C:ASP564 4.4 28.5 1.0
O C:THR633 4.5 34.4 1.0
NE2 C:HIS563 4.6 29.2 1.0
CD2 C:HIS525 4.7 37.1 1.0
CB C:THR633 4.7 30.7 1.0
CA C:ASP564 4.8 29.6 1.0
NE2 C:HIS525 4.8 38.0 1.0
CD C:GLU592 4.9 34.0 1.0
CG C:GLU592 4.9 30.3 1.0

Magnesium binding site 4 out of 4 in 5sjk

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One


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 5,8- Dichloro-2,3,4,9-Tetrahydropyrido[3,4-B]Indol-1-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:44.4
occ:1.00
 O D:HOH930 2.0 37.6 1.0
O D:HOH933 2.0 41.6 1.0
O D:HOH931 2.1 30.1 1.0
O D:HOH940 2.1 35.5 1.0
O D:HOH913 2.1 45.9 1.0
OD1 D:ASP564 2.2 46.6 1.0
CG D:ASP564 3.1 41.0 1.0
OD2 D:ASP564 3.4 46.1 1.0
ZN D:ZN801 3.8 50.5 1.0
O D:HOH941 3.9 43.8 1.0
O D:HOH935 3.9 43.4 1.0
OE2 D:GLU592 4.0 45.0 1.0
NE2 D:HIS595 4.1 41.9 1.0
CD2 D:HIS567 4.2 44.7 1.0
CD2 D:HIS595 4.3 42.6 1.0
CD2 D:HIS563 4.4 39.7 1.0
OG1 D:THR633 4.4 42.9 1.0
NE2 D:HIS567 4.4 43.3 1.0
O D:HIS563 4.4 41.4 1.0
CB D:ASP564 4.5 42.8 1.0
CD2 D:HIS525 4.6 50.6 1.0
OD2 D:ASP674 4.6 48.6 1.0
O D:THR633 4.7 45.7 1.0
NE2 D:HIS563 4.7 35.5 1.0
CA D:ASP564 4.8 39.8 1.0
NE2 D:HIS525 4.8 51.9 1.0
CB D:THR633 4.8 43.8 1.0
CD D:GLU592 4.8 48.1 1.0
CG D:GLU592 4.9 50.0 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: Tue Aug 12 20:07:50 2025

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