Atomistry » Magnesium » PDB 3py8-3q86 » 3q30
Atomistry »
  Magnesium »
    PDB 3py8-3q86 »
      3q30 »

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

Last articles

Cl in 4BF5
Cl in 4BJY
Cl in 4BJX
Cl in 4BJO
Cl in 4BJP
Cl in 4BHU
Cl in 4BJM
Cl in 4BJ3
Cl in 4BJ1
Cl in 4BIS
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy