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Magnesium in PDB 1ob5: T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna

Enzymatic activity of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna

All present enzymatic activity of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna:
3.6.1.48;

Protein crystallography data

The structure of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna, PDB code: 1ob5 was solved by C.Dahlberg, R.C.Nielsen, A.Parmeggiani, J.Nyborg, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.54 / 3.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 212.570, 122.330, 135.680, 90.00, 121.30, 90.00
R / Rfree (%) 28 / 29.4

Other elements in 1ob5:

The structure of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna also contains other interesting chemical elements:

Chlorine (Cl) 6 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna (pdb code 1ob5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna, PDB code: 1ob5:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1ob5

Go back to Magnesium Binding Sites List in 1ob5
Magnesium binding site 1 out of 3 in the T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg1407

b:57.1
occ:1.00
 OG1 A:THR25 2.2 65.2 1.0
OG1 A:THR62 2.5 46.1 1.0
O2B A:GNP1406 2.6 47.8 1.0
CB A:THR62 2.8 40.4 1.0
O1G A:GNP1406 2.9 62.1 1.0
O A:CYS82 3.0 69.3 1.0
OD2 A:ASP81 3.2 74.8 1.0
CG2 A:THR62 3.3 42.8 1.0
CB A:THR25 3.5 73.2 1.0
N A:THR25 3.5 81.2 1.0
PB A:GNP1406 3.5 66.0 1.0
CE A:LYS24 3.6 77.2 1.0
CB A:LYS24 3.8 89.3 1.0
O1B A:GNP1406 3.8 61.5 1.0
CG A:ASP81 3.8 64.2 1.0
C A:CYS82 3.9 61.9 1.0
CA A:THR25 3.9 76.4 1.0
N3B A:GNP1406 4.0 63.8 1.0
PG A:GNP1406 4.0 63.2 1.0
OD1 A:ASP81 4.0 63.0 1.0
NZ A:LYS24 4.1 72.1 1.0
CA A:PRO83 4.2 36.9 1.0
CA A:THR62 4.3 40.4 1.0
O2G A:GNP1406 4.3 67.7 1.0
C A:LYS24 4.3 83.9 1.0
N A:PRO83 4.5 49.4 1.0
CD A:LYS24 4.5 82.9 1.0
CG2 A:THR25 4.6 75.2 1.0
CA A:LYS24 4.6 84.4 1.0
N A:THR62 4.6 48.3 1.0
CG A:LYS24 4.7 88.2 1.0
N A:CYS82 4.9 65.3 1.0
C A:PRO83 4.9 26.9 1.0
N A:GLY84 5.0 34.1 1.0
CA A:CYS82 5.0 63.4 1.0
C A:ASP81 5.0 67.8 1.0
O3A A:GNP1406 5.0 62.6 1.0

Magnesium binding site 2 out of 3 in 1ob5

Go back to Magnesium Binding Sites List in 1ob5
Magnesium binding site 2 out of 3 in the T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg1407

b:57.1
occ:1.00
 OG1 C:THR25 2.2 65.2 1.0
OG1 C:THR62 2.5 46.1 1.0
O2B C:GNP1406 2.6 47.8 1.0
CB C:THR62 2.8 40.4 1.0
O1G C:GNP1406 2.9 62.1 1.0
O C:CYS82 3.0 69.3 1.0
OD2 C:ASP81 3.2 74.8 1.0
CG2 C:THR62 3.3 42.8 1.0
CB C:THR25 3.5 73.2 1.0
N C:THR25 3.5 81.2 1.0
PB C:GNP1406 3.5 66.0 1.0
CE C:LYS24 3.6 77.2 1.0
CB C:LYS24 3.8 89.3 1.0
O1B C:GNP1406 3.8 61.5 1.0
CG C:ASP81 3.8 64.2 1.0
C C:CYS82 3.9 61.9 1.0
CA C:THR25 3.9 76.4 1.0
N3B C:GNP1406 4.0 63.8 1.0
PG C:GNP1406 4.0 63.2 1.0
OD1 C:ASP81 4.0 63.0 1.0
NZ C:LYS24 4.1 72.1 1.0
CA C:PRO83 4.2 36.9 1.0
CA C:THR62 4.3 40.4 1.0
O2G C:GNP1406 4.3 67.7 1.0
C C:LYS24 4.3 83.9 1.0
N C:PRO83 4.5 49.4 1.0
CD C:LYS24 4.5 82.9 1.0
CG2 C:THR25 4.6 75.2 1.0
CA C:LYS24 4.6 84.4 1.0
N C:THR62 4.6 48.3 1.0
CG C:LYS24 4.7 88.2 1.0
N C:CYS82 4.9 65.3 1.0
C C:PRO83 4.9 26.9 1.0
N C:GLY84 5.0 34.1 1.0
CA C:CYS82 5.0 63.4 1.0
C C:ASP81 5.0 67.8 1.0
O3A C:GNP1406 5.0 62.6 1.0

Magnesium binding site 3 out of 3 in 1ob5

Go back to Magnesium Binding Sites List in 1ob5
Magnesium binding site 3 out of 3 in the T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of T. Aquaticus Elongation Factor Ef-Tu Complexed with the Antibiotic Enacyloxin Iia, A Gtp Analog, and Phe-Trna within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg1407

b:57.1
occ:1.00
 OG1 E:THR25 2.2 65.2 1.0
OG1 E:THR62 2.5 46.1 1.0
O2B E:GNP1406 2.6 47.8 1.0
CB E:THR62 2.8 40.4 1.0
O1G E:GNP1406 2.9 62.1 1.0
O E:CYS82 3.0 69.3 1.0
OD2 E:ASP81 3.2 74.8 1.0
CG2 E:THR62 3.3 42.8 1.0
CB E:THR25 3.5 73.2 1.0
N E:THR25 3.5 81.2 1.0
PB E:GNP1406 3.5 66.0 1.0
CE E:LYS24 3.6 77.2 1.0
CB E:LYS24 3.8 89.3 1.0
O1B E:GNP1406 3.8 61.5 1.0
CG E:ASP81 3.8 64.2 1.0
C E:CYS82 3.9 61.9 1.0
CA E:THR25 3.9 76.4 1.0
N3B E:GNP1406 4.0 63.8 1.0
OD1 E:ASP81 4.0 63.0 1.0
PG E:GNP1406 4.0 63.2 1.0
NZ E:LYS24 4.1 72.1 1.0
CA E:PRO83 4.2 36.9 1.0
CA E:THR62 4.3 40.4 1.0
O2G E:GNP1406 4.3 67.7 1.0
C E:LYS24 4.3 83.9 1.0
N E:PRO83 4.5 49.4 1.0
CD E:LYS24 4.5 82.9 1.0
CG2 E:THR25 4.6 75.2 1.0
CA E:LYS24 4.6 84.4 1.0
N E:THR62 4.6 48.3 1.0
CG E:LYS24 4.7 88.2 1.0
N E:CYS82 4.9 65.3 1.0
C E:PRO83 4.9 26.9 1.0
C E:ASP81 5.0 67.8 1.0
CA E:CYS82 5.0 63.4 1.0
N E:GLY84 5.0 34.1 1.0
O3A E:GNP1406 5.0 62.6 1.0

Reference:

A.Parmeggiani, I.M.Krab, T.Watanabe, R.C.Nielsen, C.Dahlberg, J.Nyborg, P.Nissen. Enacyloxin Iia Pinpoints A Binding Pocket of Elongation Factor Tu For Development of Novel Antibiotics. J.Biol.Chem. V. 281 2893 2006.
ISSN: ISSN 0021-9258
PubMed: 16257965
DOI: 10.1074/JBC.M505951200
Page generated: Tue Aug 13 10:35:20 2024

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