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Magnesium in PDB 5siv: Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide

Enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide

All present enzymatic activity of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide:
3.1.4.17;

Protein crystallography data

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide, PDB code: 5siv 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) 41.27 / 2.20
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 134.665, 134.665, 233.615, 90, 90, 120
R / Rfree (%) 19.6 / 25.6

Other elements in 5siv:

The structure of Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide 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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide (pdb code 5siv). 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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide, PDB code: 5siv:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5siv

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Magnesium binding site 1 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg802

b:27.7
occ:1.00
 O A:HOH993 1.8 22.1 1.0
O A:HOH941 2.0 30.3 1.0
O A:HOH958 2.0 23.0 1.0
O A:HOH932 2.1 28.0 1.0
OD1 A:ASP564 2.1 25.4 1.0
O A:HOH927 2.2 22.6 1.0
CG A:ASP564 3.1 24.6 1.0
OD2 A:ASP564 3.3 26.1 1.0
ZN A:ZN801 3.8 31.6 1.0
O A:HOH983 3.9 32.7 1.0
OE2 A:GLU592 4.0 36.2 1.0
NE2 A:HIS595 4.1 24.7 1.0
OG1 A:THR633 4.2 33.5 1.0
CD2 A:HIS563 4.3 23.2 1.0
O A:HOH994 4.3 33.2 1.0
CD2 A:HIS567 4.3 37.0 1.0
O A:THR633 4.4 32.1 1.0
OD2 A:ASP674 4.4 40.0 1.0
O A:HIS563 4.4 27.6 1.0
CD2 A:HIS595 4.4 24.0 1.0
CB A:ASP564 4.4 23.5 1.0
NE2 A:HIS567 4.5 39.4 1.0
NE2 A:HIS563 4.6 25.6 1.0
CB A:THR633 4.6 30.2 1.0
CD2 A:HIS525 4.7 34.1 1.0
CG A:GLU592 4.8 34.6 1.0
NE2 A:HIS525 4.8 35.5 1.0
CA A:ASP564 4.8 26.6 1.0
CD A:GLU592 4.8 39.1 1.0
O A:HOH985 4.9 39.8 1.0

Magnesium binding site 2 out of 4 in 5siv

Go back to Magnesium Binding Sites List in 5siv
Magnesium binding site 2 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg802

b:20.0
occ:1.00
 O B:HOH948 1.8 23.8 1.0
O B:HOH918 1.9 22.9 1.0
O B:HOH988 2.1 20.6 1.0
OD1 B:ASP564 2.1 23.2 1.0
O B:HOH995 2.2 22.0 1.0
O B:HOH914 2.2 16.7 1.0
CG B:ASP564 3.1 21.6 1.0
OD2 B:ASP564 3.4 24.7 1.0
ZN B:ZN801 3.7 30.1 1.0
OG1 B:THR633 4.0 30.7 1.0
OE2 B:GLU592 4.1 33.1 1.0
CD2 B:HIS563 4.1 22.6 1.0
O B:HOH971 4.1 38.6 1.0
NE2 B:HIS595 4.2 27.4 1.0
O B:HIS563 4.2 24.6 1.0
OD2 B:ASP674 4.2 28.2 1.0
O B:HOH978 4.4 30.2 1.0
CD2 B:HIS595 4.4 27.0 1.0
CD2 B:HIS567 4.4 28.1 1.0
NE2 B:HIS563 4.4 24.9 1.0
CB B:ASP564 4.4 22.6 1.0
O B:THR633 4.4 29.5 1.0
CB B:THR633 4.5 30.7 1.0
NE2 B:HIS567 4.7 29.1 1.0
CD2 B:HIS525 4.7 27.6 1.0
CG B:GLU592 4.7 30.4 1.0
CA B:ASP564 4.8 24.2 1.0
NE2 B:HIS525 4.8 30.8 1.0
CD B:GLU592 4.8 30.0 1.0
C B:HIS563 5.0 25.1 1.0

Magnesium binding site 3 out of 4 in 5siv

Go back to Magnesium Binding Sites List in 5siv
Magnesium binding site 3 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg802

b:25.0
occ:1.00
 O C:HOH972 1.9 24.9 1.0
O C:HOH936 2.0 22.6 1.0
O C:HOH1003 2.1 28.9 1.0
O C:HOH925 2.1 24.0 1.0
OD1 C:ASP564 2.1 24.2 1.0
O C:HOH938 2.2 22.0 1.0
CG C:ASP564 3.0 23.8 1.0
OD2 C:ASP564 3.3 23.6 1.0
ZN C:ZN801 3.7 31.1 1.0
OE2 C:GLU592 3.9 32.7 1.0
O C:HOH990 4.0 37.1 1.0
NE2 C:HIS595 4.1 27.7 1.0
CD2 C:HIS563 4.2 23.6 1.0
OD2 C:ASP674 4.2 32.5 1.0
CD2 C:HIS567 4.2 28.6 1.0
O C:HOH982 4.2 38.3 1.0
OG1 C:THR633 4.2 32.5 1.0
O C:HIS563 4.3 20.7 1.0
CD2 C:HIS595 4.4 29.1 1.0
CB C:ASP564 4.4 23.9 1.0
NE2 C:HIS567 4.5 30.1 1.0
O C:THR633 4.5 30.1 1.0
CD2 C:HIS525 4.6 36.1 1.0
NE2 C:HIS563 4.7 25.5 1.0
CB C:THR633 4.7 29.8 1.0
CA C:ASP564 4.8 24.6 1.0
NE2 C:HIS525 4.8 38.9 1.0
CD C:GLU592 4.9 31.1 1.0
CG C:GLU592 5.0 28.7 1.0

Magnesium binding site 4 out of 4 in 5siv

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Magnesium binding site 4 out of 4 in the Crystal Structure of Human Phosphodiesterase 10 in Complex with N- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide


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- (Thiophen-2-Ylmethyl)Quinoxaline-6-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg802

b:39.9
occ:1.00
 O D:HOH968 1.9 38.2 1.0
OD1 D:ASP564 2.1 32.7 1.0
O D:HOH959 2.2 31.9 1.0
O D:HOH922 2.2 27.3 1.0
O D:HOH928 2.2 37.0 1.0
O D:HOH935 2.3 33.1 1.0
CG D:ASP564 3.0 32.5 1.0
OD2 D:ASP564 3.4 36.7 1.0
O D:HOH966 3.8 34.6 1.0
ZN D:ZN801 3.9 38.9 1.0
O D:HOH955 3.9 36.9 1.0
CD2 D:HIS567 4.0 45.2 1.0
OE2 D:GLU592 4.0 44.5 1.0
NE2 D:HIS595 4.1 38.6 1.0
NE2 D:HIS567 4.2 43.4 1.0
CD2 D:HIS595 4.4 38.2 1.0
CB D:ASP564 4.4 30.8 1.0
CD2 D:HIS525 4.4 44.6 1.0
CD2 D:HIS563 4.4 35.5 1.0
OG1 D:THR633 4.5 31.0 1.0
OD2 D:ASP674 4.5 38.6 1.0
O D:HIS563 4.6 35.8 1.0
NE2 D:HIS525 4.7 42.3 1.0
CA D:ASP564 4.7 32.0 1.0
O D:THR633 4.8 44.0 1.0
NE2 D:HIS563 4.9 30.9 1.0
CD D:GLU592 4.9 42.8 1.0
CB D:THR633 4.9 33.8 1.0
CG D:GLU592 5.0 40.6 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 04:15:01 2024

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