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Magnesium in PDB 3weg: Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion

Enzymatic activity of Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion

All present enzymatic activity of Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion:
2.5.1.21;

Protein crystallography data

The structure of Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion, PDB code: 3weg was solved by C.I.Liu, W.Y.Jeng, A.H.J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.43 / 1.75
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 94.369, 106.721, 33.569, 90.00, 90.00, 90.00
R / Rfree (%) 15.5 / 20.8

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion (pdb code 3weg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion, PDB code: 3weg:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 3weg

Go back to Magnesium Binding Sites List in 3weg
Magnesium binding site 1 out of 3 in the Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion


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 the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:41.4
occ:1.00
 O A:HOH706 1.8 46.9 1.0
O A:HOH697 2.2 34.5 1.0
OD2 A:ASP219 2.2 20.4 1.0
O A:HOH696 2.3 32.6 1.0
O A:HOH707 2.3 42.2 1.0
CG A:ASP219 3.3 17.7 1.0
O2A A:FPS405 3.5 0.0 1.0
CB A:ASP219 3.7 15.7 1.0
O3A A:FPS405 4.0 0.4 1.0
PA A:FPS405 4.3 0.1 1.0
OE2 A:GLU222 4.3 37.6 1.0
OD1 A:ASP219 4.3 19.1 1.0
NH2 A:ARG218 4.4 27.1 1.0
OD2 A:ASP223 4.4 21.6 1.0
OD1 A:ASP223 4.4 23.6 1.0
O A:ASN215 4.4 12.9 1.0
CB A:ASN215 4.6 16.4 1.0
O3B A:FPS405 4.6 0.7 1.0
PB A:FPS405 4.7 0.5 1.0
C A:ASN215 4.8 13.4 1.0
CG A:ASP223 4.8 22.1 1.0
O2B A:FPS405 4.9 0.4 1.0

Magnesium binding site 2 out of 3 in 3weg

Go back to Magnesium Binding Sites List in 3weg
Magnesium binding site 2 out of 3 in the Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion


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 the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:33.9
occ:1.00
 OD1 A:ASP80 2.1 30.9 1.0
OE1 A:GLU83 2.2 34.0 1.0
OD1 A:ASP84 2.2 37.2 1.0
O1B A:FPS405 2.3 0.5 1.0
CG A:ASP80 3.2 29.5 1.0
CG A:ASP84 3.2 36.8 1.0
CD A:GLU83 3.4 33.0 1.0
PB A:FPS405 3.5 0.5 1.0
OD2 A:ASP80 3.6 33.6 1.0
OD2 A:ASP84 3.6 40.6 1.0
O3B A:FPS405 3.8 0.7 1.0
O2B A:FPS405 4.0 0.4 1.0
OE2 A:GLU83 4.1 31.3 1.0
MG A:MG403 4.1 66.3 1.0
O A:ASP80 4.2 27.6 1.0
OH A:TYR171 4.3 28.5 1.0
CG A:GLU83 4.3 32.5 1.0
CB A:GLU83 4.3 32.0 1.0
CB A:ASP80 4.5 26.6 1.0
CB A:ASP84 4.5 35.9 1.0
N A:ASP84 4.6 33.7 1.0
CA A:ASP80 4.7 26.5 1.0
CA A:ASP84 4.8 35.4 1.0
O1A A:FPS405 4.8 0.4 1.0
O3A A:FPS405 4.8 0.4 1.0
C A:ASP80 4.8 27.4 1.0
C3 A:FPS405 4.9 91.5 1.0
CE A:MET154 5.0 26.6 1.0

Magnesium binding site 3 out of 3 in 3weg

Go back to Magnesium Binding Sites List in 3weg
Magnesium binding site 3 out of 3 in the Crystal Structure of the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion


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 the Human Squalene Synthase in Complex with Farnesyl Thiopyrophosphate and Magnesium Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:66.3
occ:1.00
 O1A A:FPS405 1.7 0.4 1.0
OD2 A:ASP84 1.9 40.6 1.0
OD2 A:ASP80 2.2 33.6 1.0
CG A:ASP84 3.1 36.8 1.0
PA A:FPS405 3.3 0.1 1.0
O1B A:FPS405 3.3 0.5 1.0
CG A:ASP80 3.3 29.5 1.0
O3B A:FPS405 3.5 0.7 1.0
OD1 A:ASP84 3.7 37.2 1.0
PB A:FPS405 3.7 0.5 1.0
NH1 A:ARG77 3.8 39.5 1.0
OD1 A:ASP80 3.8 30.9 1.0
O3A A:FPS405 3.9 0.4 1.0
O2A A:FPS405 4.1 0.0 1.0
MG A:MG402 4.1 33.9 1.0
S1 A:FPS405 4.3 0.7 1.0
CB A:ASP84 4.3 35.9 1.0
C2 A:FPS405 4.5 94.2 1.0
CB A:ASP80 4.5 26.6 1.0
O A:ASP80 4.6 27.6 1.0
C1 A:FPS405 4.7 97.8 1.0
C A:ASP80 5.0 27.4 1.0

Reference:

C.I.Liu, W.Y.Jeng, W.J.Chang, M.F.Shih, T.P.Ko, A.H.J.Wang. Structural Insights Into the Catalytic Mechanism of Human Squalene Synthase Acta Crystallogr.,Sect.D V. 70 231 2014.
ISSN: ISSN 0907-4449
DOI: 10.1107/S1399004713026230
Page generated: Thu Aug 15 13:23:11 2024

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