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Magnesium in PDB 3aqc: M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue

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

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

Protein crystallography data

The structure of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue, PDB code: 3aqc 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 / 2.61
Space group I 21 3
Cell size a, b, c (Å), α, β, γ (°) 189.803, 189.803, 189.803, 90.00, 90.00, 90.00
R / Rfree (%) 23.8 / 28.2

Other elements in 3aqc:

The structure of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue 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 and Fpp Analogue (pdb code 3aqc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue, PDB code: 3aqc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 3aqc

Go back to Magnesium Binding Sites List in 3aqc
Magnesium binding site 1 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


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 and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg326

b:57.1
occ:1.00
 O3B B:2DE329 2.2 66.9 1.0
OD2 B:ASP88 2.2 54.2 1.0
O2A B:2DE329 2.6 65.2 1.0
OD1 B:ASP84 2.7 49.9 1.0
CG B:ASP84 3.0 49.7 1.0
OD2 B:ASP84 3.0 50.1 1.0
CG B:ASP88 3.1 54.7 1.0
CB B:ASP88 3.3 55.0 1.0
PB B:2DE329 3.6 67.2 1.0
MG B:MG327 3.8 46.6 1.0
OD1 B:ASP85 3.8 49.8 1.0
PA B:2DE329 3.9 65.0 1.0
O1B B:2DE329 4.0 67.5 1.0
O3A B:2DE329 4.1 66.1 1.0
O B:ASP84 4.1 49.9 1.0
CB B:ASP84 4.2 49.6 1.0
OD1 B:ASP88 4.2 54.7 1.0
OG B:SER90 4.2 59.4 1.0
C B:ASP84 4.2 49.9 1.0
N B:ASP85 4.5 50.1 1.0
CA B:ASP85 4.6 50.4 1.0
O1 B:2DE329 4.7 64.5 1.0
NH2 B:ARG93 4.8 62.2 1.0
O2B B:2DE329 4.8 67.2 1.0
CA B:ASP88 4.8 55.1 1.0
CA B:ASP84 4.8 49.6 1.0
CG B:ASP85 4.9 50.2 1.0
CB B:SER90 5.0 59.3 1.0

Magnesium binding site 2 out of 6 in 3aqc

Go back to Magnesium Binding Sites List in 3aqc
Magnesium binding site 2 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


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 and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg327

b:46.6
occ:1.00
 OD2 B:ASP88 2.4 54.2 1.0
OD1 B:ASP84 2.5 49.9 1.0
O2A B:2DE329 2.7 65.2 1.0
OD1 B:ASP88 3.0 54.7 1.0
CG B:ASP88 3.0 54.7 1.0
CG B:ASP84 3.2 49.7 1.0
OD2 B:ASP84 3.4 50.1 1.0
O1 B:2DE329 3.6 64.5 1.0
PA B:2DE329 3.7 65.0 1.0
OE1 B:GLU146 3.8 36.4 1.0
MG B:MG326 3.8 57.1 1.0
OE1 B:GLN149 3.9 34.8 1.0
O1A B:2DE329 4.5 65.4 1.0
CB B:ASP88 4.5 55.0 1.0
CB B:ASP84 4.5 49.6 1.0
CD B:GLU146 4.7 35.7 1.0
O B:ASP84 4.9 49.9 1.0
CA B:ASP84 4.9 49.6 1.0
C1 B:2DE329 5.0 62.7 1.0
O3B B:2DE329 5.0 66.9 1.0
OE2 B:GLU146 5.0 35.1 1.0
CD B:GLN149 5.0 34.6 1.0

Magnesium binding site 3 out of 6 in 3aqc

Go back to Magnesium Binding Sites List in 3aqc
Magnesium binding site 3 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


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 and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg328

b:54.8
occ:1.00
 OD2 B:ASP211 2.4 42.8 1.0
O B:HOH349 3.1 41.3 1.0
O1B B:2DE329 3.2 67.5 1.0
CG B:ASP211 3.6 42.7 1.0
OD1 B:ASP230 3.8 43.4 1.0
O1A B:2DE329 3.9 65.4 1.0
OD2 B:ASP230 3.9 43.0 1.0
OD1 B:ASP211 4.1 43.9 1.0
NZ B:LYS170 4.2 45.1 1.0
CG B:ASP230 4.3 43.5 1.0
O3A B:2DE329 4.3 66.1 1.0
PB B:2DE329 4.3 67.2 1.0
OE1 B:GLN208 4.4 43.0 1.0
OD1 B:ASP212 4.5 42.2 1.0
O2B B:2DE329 4.7 67.2 1.0
OD1 B:ASP215 4.7 46.9 1.0
PA B:2DE329 4.7 65.0 1.0
CB B:ASP211 4.8 42.5 1.0
O B:ASP211 4.8 42.4 1.0
NZ B:LYS225 4.9 60.7 1.0

Magnesium binding site 4 out of 6 in 3aqc

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Magnesium binding site 4 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


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 and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg327

b:50.3
occ:1.00
 O1B D:2DE330 1.9 58.4 1.0
OD1 D:ASP84 2.2 32.2 1.0
O2A D:2DE330 2.2 56.2 1.0
OD2 D:ASP88 2.3 35.1 1.0
CG D:ASP88 3.2 34.5 1.0
CG D:ASP84 3.3 31.7 1.0
PB D:2DE330 3.3 58.6 1.0
CB D:ASP88 3.4 34.2 1.0
PA D:2DE330 3.6 56.7 1.0
OD2 D:ASP84 3.7 32.4 1.0
MG D:MG328 3.7 37.5 1.0
O3A D:2DE330 3.9 57.2 1.0
O3B D:2DE330 4.1 59.3 1.0
O D:ASP84 4.1 31.3 1.0
OG D:SER90 4.1 38.6 1.0
O D:HOH358 4.2 36.3 1.0
OD1 D:ASP85 4.2 31.7 1.0
OD1 D:ASP88 4.4 34.4 1.0
O2B D:2DE330 4.4 58.9 1.0
C D:ASP84 4.5 31.4 1.0
O1A D:2DE330 4.5 56.2 1.0
CB D:ASP84 4.5 31.4 1.0
O1 D:2DE330 4.6 56.1 1.0
NH1 D:ARG93 4.8 41.4 1.0
C1 D:2DE330 4.8 55.0 1.0
CA D:ASP88 4.9 34.5 1.0
N D:ASP85 4.9 31.5 1.0
CA D:ASP85 5.0 31.8 1.0

Magnesium binding site 5 out of 6 in 3aqc

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Magnesium binding site 5 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg328

b:37.5
occ:1.00
 OD2 D:ASP84 2.1 32.4 1.0
O D:HOH358 2.2 36.3 1.0
O2A D:2DE330 2.3 56.2 1.0
O D:HOH349 2.3 30.6 1.0
OD2 D:ASP88 2.4 35.1 1.0
PA D:2DE330 3.0 56.7 1.0
CG D:ASP84 3.1 31.7 1.0
O1A D:2DE330 3.3 56.2 1.0
CG D:ASP88 3.3 34.5 1.0
O1 D:2DE330 3.3 56.1 1.0
OE2 D:GLU146 3.4 35.0 1.0
OD1 D:ASP84 3.4 32.2 1.0
OD1 D:ASP88 3.5 34.4 1.0
MG D:MG327 3.7 50.3 1.0
C1 D:2DE330 4.3 55.0 1.0
NE2 D:GLN149 4.3 37.9 1.0
OE1 D:GLN149 4.3 37.3 1.0
NZ D:LYS170 4.4 36.4 1.0
O1B D:2DE330 4.4 58.4 1.0
C2 D:2DE330 4.4 54.0 1.0
CB D:ASP84 4.4 31.4 1.0
O3A D:2DE330 4.5 57.2 1.0
CD D:GLU146 4.6 34.0 1.0
CD D:GLN149 4.7 36.9 1.0
CB D:ASP88 4.7 34.2 1.0
O D:ASP84 5.0 31.3 1.0

Magnesium binding site 6 out of 6 in 3aqc

Go back to Magnesium Binding Sites List in 3aqc
Magnesium binding site 6 out of 6 in the M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of M. Luteus B-P 26 Heterodimeric Hexaprenyl Diphosphate Synthase in Complex with Magnesium and Fpp Analogue within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg329

b:63.4
occ:1.00
 OD2 D:ASP211 2.3 38.3 1.0
O D:HOH336 2.4 45.2 1.0
CG D:ASP211 3.3 37.5 1.0
NZ D:LYS225 3.6 49.7 1.0
OD1 D:ASP211 3.7 37.6 1.0
OD2 D:ASP230 4.1 39.8 1.0
O D:ASP211 4.2 37.8 1.0
OD1 D:ASP215 4.2 42.4 1.0
O3B D:2DE330 4.2 59.3 1.0
OD1 D:ASP230 4.3 41.4 1.0
CB D:ASP211 4.5 37.3 1.0
CE D:LYS225 4.5 49.3 1.0
O3A D:2DE330 4.6 57.2 1.0
C D:ASP211 4.6 37.6 1.0
CG D:ASP230 4.6 40.6 1.0
OD1 D:ASP212 4.7 38.9 1.0
OE1 D:GLN208 4.7 36.4 1.0
CG D:ASP215 5.0 41.8 1.0
CB D:ASP215 5.0 41.7 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 08:42:35 2024

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