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Magnesium in PDB 3q30: Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid

Enzymatic activity of Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid

All present enzymatic activity of Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid:
2.5.1.21;

Protein crystallography data

The structure of Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid, PDB code: 3q30 was solved by M.Suzuki, H.Shimizu, S.Katakura, K.Yamazaki, N.Higashihashi, M.Ichikawa, A.Yokomizo, M.Itoh, K.Sugita, H.Usui, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.00 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 85.973, 59.526, 84.139, 90.00, 115.71, 90.00
R / Rfree (%) 20.7 / 23.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid (pdb code 3q30). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid, PDB code: 3q30:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 3q30

Go back to Magnesium Binding Sites List in 3q30
Magnesium binding site 1 out of 2 in the Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg600

b:37.7
occ:1.00
 O A:HOH461 1.9 33.2 1.0
OD1 A:ASP80 2.0 27.8 1.0
OE1 A:GLU83 2.1 32.5 1.0
O43 A:D61700 2.2 35.6 1.0
O A:HOH506 2.3 28.8 1.0
OD1 A:ASP84 2.3 29.2 1.0
CG A:ASP80 3.1 29.8 1.0
CD A:GLU83 3.2 30.1 1.0
C42 A:D61700 3.2 37.2 1.0
CG A:ASP84 3.4 27.5 1.0
MG A:MG601 3.5 32.5 1.0
OD2 A:ASP80 3.5 29.2 1.0
O44 A:D61700 3.6 39.1 1.0
OE2 A:GLU83 3.8 29.1 1.0
OD2 A:ASP84 3.8 28.3 1.0
O A:HOH492 3.8 34.0 1.0
CB A:GLU83 4.3 26.1 1.0
CG A:GLU83 4.3 27.4 1.0
O A:ASP80 4.3 28.3 1.0
O A:HOH599 4.4 32.8 1.0
CB A:ASP80 4.4 27.2 1.0
C36 A:D61700 4.5 36.8 1.0
N A:ASP84 4.5 24.7 1.0
O A:HOH418 4.5 56.6 1.0
OH A:TYR171 4.6 28.9 1.0
O20 A:D61700 4.6 33.7 1.0
CE A:MET154 4.6 23.9 1.0
CB A:ASP84 4.6 26.6 1.0
CA A:ASP84 4.7 25.9 1.0
O37 A:D61700 4.8 37.3 1.0
CA A:ASP80 4.8 27.9 1.0
C21 A:D61700 4.8 32.8 1.0
C A:GLU83 4.9 24.6 1.0
C A:ASP80 5.0 27.4 1.0

Magnesium binding site 2 out of 2 in 3q30

Go back to Magnesium Binding Sites List in 3q30
Magnesium binding site 2 out of 2 in the Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Squalene Synthase in Complex with (2R,3R)-2-Carboxymethoxy-3-[5- (2-Naphthalenyl)Pentyl]Aminocarbonyl-3-[5-(2-Naphthalenyl) Pentyloxy]Propionic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg601

b:32.5
occ:1.00
 O A:HOH599 1.9 32.8 1.0
OD2 A:ASP80 2.1 29.2 1.0
OD2 A:ASP84 2.1 28.3 1.0
O43 A:D61700 2.1 35.6 1.0
O41 A:D61700 2.1 34.6 1.0
O37 A:D61700 2.4 37.3 1.0
C39 A:D61700 2.9 37.4 1.0
C42 A:D61700 3.0 37.2 1.0
CG A:ASP84 3.0 27.5 1.0
C38 A:D61700 3.0 36.7 1.0
CG A:ASP80 3.0 29.8 1.0
OD1 A:ASP84 3.1 29.2 1.0
C36 A:D61700 3.2 36.8 1.0
OD1 A:ASP80 3.3 27.8 1.0
MG A:MG600 3.5 37.7 1.0
NH1 A:ARG77 3.9 40.6 1.0
O20 A:D61700 4.1 33.7 1.0
O40 A:D61700 4.2 36.9 1.0
O44 A:D61700 4.2 39.1 1.0
O A:HOH535 4.2 39.6 1.0
O A:HOH506 4.3 28.8 1.0
C19 A:D61700 4.3 36.5 1.0
CB A:ASP84 4.4 26.6 1.0
CB A:ASP80 4.4 27.2 1.0
O A:ASP80 4.7 28.3 1.0
O A:HOH461 4.7 33.2 1.0
O A:HOH540 4.9 81.2 1.0

Reference:

M.Ichikawa, A.Yokomizo, M.Itoh, K.Sugita, H.Usui, H.Shimizu, M.Suzuki, K.Terayama, A.Kanda. Discovery of A New 2-Aminobenzhydrol Template For Highly Potent Squalene Synthase Inhibitors Bioorg.Med.Chem. V. 19 1930 2011.
ISSN: ISSN 0968-0896
PubMed: 21353782
DOI: 10.1016/J.BMC.2011.01.065
Page generated: Thu Aug 15 09:53:17 2024

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