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Magnesium in PDB 3lee: Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652

Enzymatic activity of Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652

All present enzymatic activity of Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652:
2.5.1.21;

Protein crystallography data

The structure of Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652, PDB code: 3lee was solved by Y.-L.Liu, F.-Y.Lin, E.Oldfield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.58 / 3.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 85.662, 153.422, 92.904, 90.00, 90.50, 90.00
R / Rfree (%) 19.1 / 27.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652 (pdb code 3lee). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652, PDB code: 3lee:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3lee

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Magnesium binding site 1 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


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 Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg452

b:40.2
occ:1.00
 OD2 A:ASP84 2.3 60.8 1.0
OE2 A:GLU83 2.3 50.1 1.0
OAC A:B65451 2.6 78.2 1.0
OD2 A:ASP80 2.7 47.0 1.0
OD1 A:ASP84 2.9 61.6 1.0
CG A:ASP84 2.9 58.5 1.0
OAA A:B65451 3.0 78.2 1.0
CD A:GLU83 3.0 51.8 1.0
PAX A:B65451 3.3 78.5 1.0
CG A:GLU83 3.4 49.4 1.0
CG A:ASP80 3.5 43.6 1.0
OD1 A:ASP80 3.6 49.4 1.0
OH A:TYR171 3.7 54.0 1.0
OE1 A:GLU83 3.9 54.8 1.0
OAB A:B65451 4.2 77.7 1.0
CB A:ASP84 4.4 53.7 1.0
OAE A:B65451 4.6 75.6 1.0
CAW A:B65451 4.8 77.4 1.0
NH1 A:ARG228 4.8 69.8 1.0
CB A:ASP80 4.9 39.0 1.0
CB A:GLU83 4.9 46.9 1.0
CA A:ASP84 4.9 52.6 1.0

Magnesium binding site 2 out of 6 in 3lee

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Magnesium binding site 2 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


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 Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg452

b:37.5
occ:1.00
 OD1 B:ASP84 2.2 51.3 1.0
OD1 B:ASP80 2.3 46.2 1.0
OAA B:B65451 2.6 80.8 1.0
OAC B:B65451 2.8 79.3 1.0
OE1 B:GLU83 2.9 58.2 1.0
CG B:ASP84 3.0 50.9 1.0
PAX B:B65451 3.0 81.3 1.0
OD2 B:ASP84 3.1 51.4 1.0
CG B:ASP80 3.4 42.8 1.0
CD B:GLU83 3.6 55.5 1.0
OAB B:B65451 3.6 79.5 1.0
OD2 B:ASP80 3.7 42.3 1.0
OE2 B:GLU83 4.0 58.0 1.0
O B:ASP80 4.4 43.2 1.0
CB B:ASP84 4.4 50.2 1.0
CB B:GLU83 4.6 47.1 1.0
CB B:ASP80 4.7 40.1 1.0
CG B:GLU83 4.7 51.3 1.0
CAW B:B65451 4.7 82.8 1.0
N B:ASP84 4.8 51.3 1.0
CA B:ASP84 4.9 50.3 1.0
OH B:TYR171 4.9 53.9 1.0
O B:HOH5 4.9 37.8 1.0

Magnesium binding site 3 out of 6 in 3lee

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Magnesium binding site 3 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


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 Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg452

b:52.6
occ:1.00
 OAC C:B65451 2.2 91.1 1.0
OD2 C:ASP80 2.3 40.8 1.0
OD1 C:ASP84 2.6 53.7 1.0
OE1 C:GLU83 2.7 57.7 1.0
OAA C:B65451 2.8 90.9 1.0
PAX C:B65451 3.0 92.4 1.0
OD2 C:ASP84 3.3 53.9 1.0
CG C:ASP84 3.3 51.6 1.0
CG C:ASP80 3.5 38.5 1.0
CD C:GLU83 3.9 55.0 1.0
OH C:TYR171 3.9 55.8 1.0
OAB C:B65451 4.0 92.0 1.0
OD1 C:ASP80 4.1 37.7 1.0
CAW C:B65451 4.4 91.2 1.0
CAR C:B65451 4.5 88.1 1.0
OE2 C:GLU83 4.6 56.3 1.0
CB C:ASP80 4.6 35.0 1.0
O C:ASP80 4.7 35.6 1.0
OAE C:B65451 4.7 92.1 1.0
CG C:GLU83 4.8 50.7 1.0
CB C:ASP84 4.8 48.0 1.0
CB C:GLU83 4.9 46.9 1.0
CG1 C:VAL175 5.0 39.8 1.0

Magnesium binding site 4 out of 6 in 3lee

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Magnesium binding site 4 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


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 the Human Squalene Synthase Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg452

b:34.4
occ:1.00
 OD2 D:ASP84 2.3 62.9 1.0
OAC D:B65451 2.5 88.7 1.0
OD2 D:ASP80 2.7 53.9 1.0
OAE D:B65451 2.8 89.7 1.0
O D:HOH395 2.9 30.9 1.0
CG D:ASP84 3.2 64.1 1.0
OD1 D:ASP80 3.4 53.7 1.0
CG D:ASP80 3.5 50.4 1.0
OAF D:B65451 3.5 91.7 1.0
SAY D:B65451 3.7 91.1 1.0
PAX D:B65451 3.9 89.9 1.0
OD1 D:ASP84 3.9 65.4 1.0
CB D:ASP84 4.1 64.5 1.0
CAW D:B65451 4.3 89.2 1.0
O D:ASP80 4.5 51.1 1.0
OE2 D:GLU83 4.6 56.2 1.0
NH1 D:ARG77 4.6 52.5 1.0
CAR D:B65451 4.7 87.5 1.0
OAA D:B65451 4.8 88.5 1.0
OAB D:B65451 4.8 89.4 1.0
NH1 D:ARG228 4.9 0.4 1.0
CB D:ASP80 4.9 46.8 1.0
OAD D:B65451 5.0 91.1 1.0

Magnesium binding site 5 out of 6 in 3lee

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Magnesium binding site 5 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg452

b:81.3
occ:1.00
 OH E:TYR171 2.2 71.4 1.0
OAA E:B65451 2.5 87.2 1.0
OE1 E:GLU83 2.7 80.1 1.0
OE2 E:GLU83 2.8 81.6 1.0
CD E:GLU83 3.1 81.3 1.0
CZ E:TYR171 3.2 71.4 1.0
CG1 E:VAL175 3.5 65.3 1.0
PAX E:B65451 3.6 87.8 1.0
OAB E:B65451 3.7 86.5 1.0
CE1 E:TYR171 3.9 71.8 1.0
CB E:VAL175 3.9 63.8 1.0
CE2 E:TYR171 4.2 70.9 1.0
OAC E:B65451 4.2 87.1 1.0
OD2 E:ASP80 4.4 66.6 1.0
CG2 E:VAL175 4.4 63.6 1.0
OD1 E:ASP84 4.4 92.6 1.0
CG E:GLU83 4.6 81.7 1.0
CE E:MET154 4.7 80.2 1.0

Magnesium binding site 6 out of 6 in 3lee

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Magnesium binding site 6 out of 6 in the Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Crystal Structure of the Human Squalene Synthase Complexed with Bph- 652 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg452

b:81.3
occ:1.00
 OAC F:B65451 2.5 0.2 1.0
OAB F:B65451 2.5 0.7 1.0
OD1 F:ASP84 2.6 0.6 1.0
PAX F:B65451 2.8 0.6 1.0
OD1 F:ASP80 2.8 76.6 1.0
OE1 F:GLU83 3.1 0.1 1.0
OAA F:B65451 3.4 0.3 1.0
CG F:ASP84 3.5 0.1 1.0
OD2 F:ASP84 3.6 0.5 1.0
O F:HOH377 3.7 53.8 1.0
CG F:ASP80 3.7 74.2 1.0
OD2 F:ASP80 4.0 75.2 1.0
CD F:GLU83 4.0 0.4 1.0
CAW F:B65451 4.5 0.9 1.0
OAE F:B65451 4.6 0.3 1.0
OE2 F:GLU83 4.7 0.9 1.0
OH F:TYR171 4.8 88.8 1.0
CB F:ASP84 4.8 0.4 1.0
CG F:GLU83 4.9 0.3 1.0
SAY F:B65451 5.0 0.6 1.0

Reference:

F.-Y.Lin, C.-I.Liu, Y.-L.Liu, Y.Zhang, K.Wang, R.Cao, A.H.J.Wang, E.Oldfield. Mechanism of Action (and Inhibition) of Head-to-Head Terpene Synthases: A Structural Investigation To Be Published.
Page generated: Wed Aug 14 18:31:17 2024

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