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Magnesium in PDB 3aqb: M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium

Enzymatic activity of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium

All present enzymatic activity of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium:
2.5.1.33;

Protein crystallography data

The structure of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium, PDB code: 3aqb was solved by D.Sasaki, M.Fujihashi, N.Okuyama, Y.Kobayashi, M.Noike, T.Koyama, K.Miki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 189.613, 189.613, 189.613, 90.00, 90.00, 90.00
R / Rfree (%) 24 / 27.6

Other elements in 3aqb:

The structure of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium (pdb code 3aqb). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium, PDB code: 3aqb:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3aqb

Go back to Magnesium Binding Sites List in 3aqb
Magnesium binding site 1 out of 4 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg326

b:44.3
occ:1.00
 OD2 B:ASP88 2.3 48.8 1.0
OD1 B:ASP84 2.3 43.7 1.0
CG B:ASP88 3.2 48.9 1.0
CG B:ASP84 3.3 43.8 1.0
OD1 B:ASP88 3.4 48.6 1.0
OD2 B:ASP84 3.6 44.0 1.0
OE1 B:GLU146 3.9 32.2 1.0
CB B:ASP88 4.6 49.2 1.0
CB B:ASP84 4.6 43.8 1.0
OE1 B:GLN149 4.8 37.4 1.0
CD B:GLU146 4.9 32.4 1.0

Magnesium binding site 2 out of 4 in 3aqb

Go back to Magnesium Binding Sites List in 3aqb
Magnesium binding site 2 out of 4 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg327

b:54.7
occ:1.00
 OD2 B:ASP211 2.3 36.5 1.0
CG B:ASP211 3.4 35.7 1.0
OD1 B:ASP211 3.9 36.5 1.0
OD1 B:ASP230 4.1 33.0 1.0
OD2 B:ASP230 4.3 32.1 1.0
NE2 B:GLN208 4.4 36.8 1.0
OD1 B:ASP212 4.5 35.1 1.0
NZ B:LYS170 4.6 35.3 1.0
O B:ASP211 4.6 35.2 1.0
CG B:ASP230 4.6 33.1 1.0
CB B:ASP211 4.6 35.4 1.0
C B:ASP211 4.9 35.3 1.0
OD1 B:ASP215 4.9 38.7 1.0

Magnesium binding site 3 out of 4 in 3aqb

Go back to Magnesium Binding Sites List in 3aqb
Magnesium binding site 3 out of 4 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg326

b:48.3
occ:1.00
 OD2 D:ASP84 2.2 30.2 1.0
OD2 D:ASP88 2.2 35.6 1.0
O D:HOH366 2.4 37.7 1.0
CG D:ASP84 2.9 29.9 1.0
OD1 D:ASP84 3.0 30.4 1.0
CG D:ASP88 3.4 35.1 1.0
OD1 D:ASP88 4.0 34.5 1.0
OE2 D:GLU146 4.2 30.2 1.0
CB D:ASP84 4.4 29.6 1.0
NZ D:LYS170 4.4 29.9 1.0
CB D:ASP88 4.6 35.0 1.0
NE2 D:GLN149 4.6 35.0 1.0
O D:ASP84 4.8 30.1 1.0
O D:HOH374 4.9 53.2 1.0

Magnesium binding site 4 out of 4 in 3aqb

Go back to Magnesium Binding Sites List in 3aqb
Magnesium binding site 4 out of 4 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg327

b:50.2
occ:1.00
 O D:HOH348 2.1 37.2 1.0
OD2 D:ASP211 2.2 32.7 1.0
O D:HOH368 2.6 38.9 1.0
CG D:ASP211 3.3 32.2 1.0
OD2 D:ASP230 3.5 36.6 1.0
O D:ASP211 3.6 32.2 1.0
OD1 D:ASP230 3.8 36.6 1.0
OD1 D:ASP211 3.9 32.9 1.0
NZ D:LYS225 3.9 49.3 1.0
C D:ASP211 4.0 32.1 1.0
CG D:ASP230 4.1 36.3 1.0
OD1 D:ASP212 4.1 32.0 1.0
CB D:ASP211 4.3 31.9 1.0
OD1 D:ASP215 4.3 38.5 1.0
CB D:ASP215 4.4 37.8 1.0
OE1 D:GLN208 4.5 30.2 1.0
N D:ASP212 4.5 32.3 1.0
CA D:ASP212 4.6 32.6 1.0
CG D:ASP215 4.6 38.1 1.0
O D:HOH332 4.7 36.7 1.0
CA D:ASP211 4.8 31.9 1.0
O D:HOH374 4.9 53.2 1.0
CE D:LYS225 4.9 49.0 1.0

Reference:

D.Sasaki, M.Fujihashi, N.Okuyama, Y.Kobayashi, M.Noike, T.Koyama, K.Miki. Crystal Structure of Heterodimeric Hexaprenyl Diphosphate Synthase From Micrococcus Luteus B-P 26 Reveals That the Small Subunit Is Directly Involved in the Product Chain Length Regulation. J.Biol.Chem. V. 286 3729 2011.
ISSN: ISSN 0021-9258
PubMed: 21068379
DOI: 10.1074/JBC.M110.147991
Page generated: Wed Aug 14 08:42:31 2024

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