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Magnesium in PDB 5skb: Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One:
3.1.4.17;

Protein crystallography data

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

Resolution Low / High (Å) 35.37 / 2.35
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 135.431, 135.431, 234.211, 90, 90, 120
R / Rfree (%) 18.8 / 24.9

Other elements in 5skb:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One 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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One (pdb code 5skb). 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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One, PDB code: 5skb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5skb

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:34.6
occ:1.00
 O A:HOH923 1.9 32.6 1.0
O A:HOH963 1.9 29.8 1.0
O A:HOH927 2.0 36.2 1.0
O A:HOH920 2.0 29.1 1.0
O A:HOH924 2.1 29.1 1.0
OD1 A:ASP564 2.1 35.2 1.0
CG A:ASP564 3.0 31.4 1.0
OD2 A:ASP564 3.2 34.3 1.0
ZN A:ZN801 3.8 40.1 1.0
OE2 A:GLU592 3.9 42.9 1.0
O A:HOH948 4.0 42.4 1.0
NE2 A:HIS595 4.1 36.4 1.0
CD2 A:HIS567 4.2 37.9 1.0
OG1 A:THR633 4.3 40.6 1.0
CD2 A:HIS563 4.3 34.9 1.0
O A:HIS563 4.3 37.3 1.0
CB A:ASP564 4.4 30.2 1.0
CD2 A:HIS595 4.4 36.2 1.0
OD2 A:ASP674 4.5 44.2 1.0
NE2 A:HIS567 4.5 40.2 1.0
O A:THR633 4.5 43.3 1.0
CD2 A:HIS525 4.6 37.8 1.0
NE2 A:HIS563 4.6 32.3 1.0
NE2 A:HIS525 4.7 38.5 1.0
CB A:THR633 4.7 38.0 1.0
CD A:GLU592 4.8 45.3 1.0
CA A:ASP564 4.8 33.7 1.0

Magnesium binding site 2 out of 4 in 5skb

Go back to Magnesium Binding Sites List in 5skb
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:29.6
occ:1.00
 O B:HOH968 2.0 27.8 1.0
O B:HOH913 2.0 33.4 1.0
O B:HOH933 2.0 29.3 1.0
O B:HOH935 2.0 29.3 1.0
O B:HOH901 2.1 28.1 1.0
OD1 B:ASP564 2.1 30.4 1.0
CG B:ASP564 3.1 29.4 1.0
OD2 B:ASP564 3.4 30.8 1.0
ZN B:ZN801 3.9 38.3 1.0
OE2 B:GLU592 3.9 37.8 1.0
NE2 B:HIS595 4.1 34.0 1.0
O B:HOH957 4.1 35.4 1.0
O B:HOH941 4.2 47.6 1.0
CD2 B:HIS567 4.2 38.5 1.0
OG1 B:THR633 4.3 35.4 1.0
CD2 B:HIS563 4.3 31.2 1.0
CD2 B:HIS595 4.3 38.1 1.0
NE2 B:HIS567 4.4 38.3 1.0
OD2 B:ASP674 4.4 38.9 1.0
CB B:ASP564 4.5 27.7 1.0
O B:THR633 4.6 34.5 1.0
O B:HIS563 4.6 33.4 1.0
NE2 B:HIS563 4.6 31.0 1.0
CD2 B:HIS525 4.6 36.0 1.0
CB B:THR633 4.7 34.0 1.0
NE2 B:HIS525 4.7 37.0 1.0
CD B:GLU592 4.7 40.1 1.0
CG B:GLU592 4.8 41.5 1.0
CA B:ASP564 4.9 30.8 1.0

Magnesium binding site 3 out of 4 in 5skb

Go back to Magnesium Binding Sites List in 5skb
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:30.3
occ:1.00
 O C:HOH960 1.9 33.0 1.0
O C:HOH983 2.0 36.2 1.0
OD1 C:ASP564 2.0 32.9 1.0
O C:HOH917 2.0 35.6 1.0
O C:HOH929 2.1 29.6 1.0
O C:HOH949 2.2 25.8 1.0
CG C:ASP564 3.0 36.7 1.0
OD2 C:ASP564 3.4 38.5 1.0
ZN C:ZN801 3.8 38.7 1.0
O C:HOH936 4.0 36.1 1.0
CD2 C:HIS567 4.1 37.2 1.0
NE2 C:HIS595 4.1 34.3 1.0
OE2 C:GLU592 4.1 40.2 1.0
CD2 C:HIS563 4.2 32.1 1.0
NE2 C:HIS567 4.3 34.4 1.0
OG1 C:THR633 4.3 34.5 1.0
O C:HIS563 4.4 33.5 1.0
CD2 C:HIS595 4.4 32.5 1.0
CB C:ASP564 4.4 33.7 1.0
OD2 C:ASP674 4.4 35.5 1.0
NE2 C:HIS563 4.5 36.8 1.0
O C:THR633 4.5 39.9 1.0
O C:HOH934 4.5 42.8 1.0
CD2 C:HIS525 4.6 41.1 1.0
NE2 C:HIS525 4.6 43.8 1.0
CA C:ASP564 4.8 33.6 1.0
CB C:THR633 4.8 34.9 1.0
CG C:GLU592 4.8 37.3 1.0
CD C:GLU592 4.9 40.6 1.0

Magnesium binding site 4 out of 4 in 5skb

Go back to Magnesium Binding Sites List in 5skb
Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-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 9- Methoxy-3,5-Dihydropyrimido[5,4-B]Indol-4-One within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:40.7
occ:1.00
 O D:HOH933 1.9 40.7 1.0
O D:HOH936 2.0 39.6 1.0
O D:HOH918 2.0 39.1 1.0
O D:HOH925 2.1 40.5 1.0
O D:HOH932 2.1 40.2 1.0
OD1 D:ASP564 2.2 39.7 1.0
CG D:ASP564 3.2 40.7 1.0
OD2 D:ASP564 3.5 45.9 1.0
ZN D:ZN801 3.7 48.7 1.0
O D:HOH937 3.7 39.2 1.0
OE2 D:GLU592 4.0 46.8 1.0
OG1 D:THR633 4.3 40.5 1.0
O D:HOH948 4.3 46.3 1.0
NE2 D:HIS595 4.3 45.5 1.0
CD2 D:HIS563 4.4 37.1 1.0
OD2 D:ASP674 4.4 58.8 1.0
O D:THR633 4.4 46.9 1.0
CD2 D:HIS567 4.4 47.8 1.0
CD2 D:HIS525 4.5 53.4 1.0
NE2 D:HIS525 4.5 53.0 1.0
CB D:THR633 4.5 44.4 1.0
CD2 D:HIS595 4.5 46.3 1.0
NE2 D:HIS567 4.6 43.4 1.0
CB D:ASP564 4.6 40.6 1.0
O D:HIS563 4.6 41.9 1.0
NE2 D:HIS563 4.7 34.7 1.0
OD1 D:ASP674 4.9 51.0 1.0
CA D:ASP564 4.9 41.2 1.0
CD D:GLU592 5.0 45.7 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 04:32:56 2024

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