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Chlorine 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:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 6 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 1 out of 6 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 Chlorine with other atoms in the Cl 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:Cl1408

b:67.7
occ:1.00
 CL30 A:ENX1408 0.0 67.7 1.0
C6 A:ENX1408 1.8 70.4 1.0
C7 A:ENX1408 2.7 68.0 1.0
C5 A:ENX1408 2.7 74.8 1.0
O A:PHE386 2.8 77.3 1.0
C A:PHE386 3.0 79.3 1.0
O31 A:ENX1408 3.1 84.1 1.0
C8 A:ENX1408 3.1 58.8 1.0
C4 A:ENX1408 3.2 75.6 1.0
N A:PHE386 3.4 83.8 1.0
CA A:PHE386 3.5 81.2 1.0
N A:ALA387 3.5 76.1 1.0
CA A:ALA387 4.0 73.4 1.0
C A:ARG385 4.0 79.3 1.0
CB A:ALA397 4.0 82.9 1.0
O29 A:ENX1408 4.0 86.9 1.0
CB A:ALA387 4.1 67.3 1.0
CB A:ARG385 4.3 69.6 1.0
O A:GLY398 4.3 72.6 1.0
N A:GLY398 4.3 79.6 1.0
O A:ARG385 4.4 75.7 1.0
C3 A:ENX1408 4.5 79.2 1.0
C9 A:ENX1408 4.6 68.0 1.0
CA A:ALA397 4.6 76.9 1.0
CA A:ARG385 4.6 75.0 1.0
CG A:ARG385 4.9 78.9 1.0
C A:ALA397 5.0 81.5 1.0
CB A:PHE386 5.0 82.3 1.0

Chlorine binding site 2 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 2 out of 6 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 Chlorine with other atoms in the Cl 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
A:Cl1408

b:75.4
occ:1.00
 CL35 A:ENX1408 0.0 75.4 1.0
C13 A:ENX1408 1.7 73.0 1.0
C14 A:ENX1408 2.7 58.2 1.0
C12 A:ENX1408 2.8 81.0 1.0
C11 A:ENX1408 3.1 79.3 1.0
C15 A:ENX1408 3.1 52.0 1.0
CD2 A:LEU323 3.3 47.4 1.0
CG A:LEU323 3.4 34.0 1.0
C34 A:ENX1408 3.4 77.8 1.0
O33 A:ENX1408 3.4 76.7 1.0
CD1 A:LEU323 3.9 41.2 1.0
C16 A:ENX1408 4.5 53.1 1.0
O A:GLN125 4.5 53.0 1.0
C10 A:ENX1408 4.6 77.6 1.0
CD2 A:TYR321 4.6 48.2 1.0
CE2 A:TYR321 4.6 46.5 1.0
CB A:ALA397 4.7 82.9 1.0
CB A:LEU323 4.7 39.9 1.0
CA A:GLN125 4.8 56.4 1.0
OE2 A:GLU327 5.0 54.1 1.0

Chlorine binding site 3 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 3 out of 6 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 Chlorine with other atoms in the Cl 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
C:Cl1408

b:67.7
occ:1.00
 CL30 C:ENX1408 0.0 67.7 1.0
C6 C:ENX1408 1.8 70.4 1.0
C7 C:ENX1408 2.7 68.0 1.0
C5 C:ENX1408 2.7 74.8 1.0
O C:PHE386 2.8 77.3 1.0
C C:PHE386 3.0 79.3 1.0
O31 C:ENX1408 3.1 84.1 1.0
C8 C:ENX1408 3.1 58.8 1.0
C4 C:ENX1408 3.2 75.6 1.0
N C:PHE386 3.4 83.8 1.0
CA C:PHE386 3.5 81.2 1.0
N C:ALA387 3.5 76.1 1.0
CA C:ALA387 4.0 73.4 1.0
C C:ARG385 4.0 79.3 1.0
CB C:ALA397 4.0 82.9 1.0
O29 C:ENX1408 4.0 86.9 1.0
CB C:ALA387 4.1 67.3 1.0
CB C:ARG385 4.3 69.6 1.0
O C:GLY398 4.3 72.6 1.0
N C:GLY398 4.3 79.6 1.0
O C:ARG385 4.4 75.7 1.0
C3 C:ENX1408 4.5 79.2 1.0
C9 C:ENX1408 4.6 68.0 1.0
CA C:ALA397 4.6 76.9 1.0
CA C:ARG385 4.6 75.0 1.0
CG C:ARG385 4.9 78.9 1.0
C C:ALA397 5.0 81.5 1.0
CB C:PHE386 5.0 82.3 1.0

Chlorine binding site 4 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 4 out of 6 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl1408

b:75.4
occ:1.00
 CL35 C:ENX1408 0.0 75.4 1.0
C13 C:ENX1408 1.7 73.0 1.0
C14 C:ENX1408 2.7 58.2 1.0
C12 C:ENX1408 2.8 81.0 1.0
C11 C:ENX1408 3.1 79.3 1.0
C15 C:ENX1408 3.1 52.0 1.0
CD2 C:LEU323 3.3 47.4 1.0
C34 C:ENX1408 3.4 77.8 1.0
CG C:LEU323 3.4 34.0 1.0
O33 C:ENX1408 3.4 76.7 1.0
CD1 C:LEU323 3.9 41.2 1.0
C16 C:ENX1408 4.5 53.1 1.0
O C:GLN125 4.5 53.0 1.0
C10 C:ENX1408 4.6 77.6 1.0
CD2 C:TYR321 4.6 48.2 1.0
CE2 C:TYR321 4.6 46.5 1.0
CB C:ALA397 4.7 82.9 1.0
CB C:LEU323 4.7 39.9 1.0
CA C:GLN125 4.8 56.4 1.0
OE2 C:GLU327 5.0 54.1 1.0

Chlorine binding site 5 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 5 out of 6 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 Chlorine with other atoms in the Cl binding site number 5 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:Cl1408

b:67.7
occ:1.00
 CL30 E:ENX1408 0.0 67.7 1.0
C6 E:ENX1408 1.8 70.4 1.0
C7 E:ENX1408 2.7 68.0 1.0
C5 E:ENX1408 2.7 74.8 1.0
O E:PHE386 2.8 77.3 1.0
C E:PHE386 3.0 79.3 1.0
O31 E:ENX1408 3.1 84.1 1.0
C8 E:ENX1408 3.1 58.8 1.0
C4 E:ENX1408 3.2 75.6 1.0
N E:PHE386 3.4 83.8 1.0
CA E:PHE386 3.5 81.2 1.0
N E:ALA387 3.5 76.1 1.0
CA E:ALA387 4.0 73.4 1.0
C E:ARG385 4.0 79.3 1.0
CB E:ALA397 4.0 82.9 1.0
O29 E:ENX1408 4.0 86.9 1.0
CB E:ALA387 4.1 67.3 1.0
CB E:ARG385 4.3 69.6 1.0
O E:GLY398 4.3 72.6 1.0
N E:GLY398 4.3 79.6 1.0
O E:ARG385 4.4 75.7 1.0
C3 E:ENX1408 4.5 79.2 1.0
C9 E:ENX1408 4.6 68.0 1.0
CA E:ALA397 4.6 76.9 1.0
CA E:ARG385 4.6 75.0 1.0
CG E:ARG385 4.9 78.9 1.0
C E:ALA397 5.0 81.5 1.0
CB E:PHE386 5.0 82.3 1.0

Chlorine binding site 6 out of 6 in 1ob5

Go back to Chlorine Binding Sites List in 1ob5
Chlorine binding site 6 out of 6 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 Chlorine with other atoms in the Cl binding site number 6 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:Cl1408

b:75.4
occ:1.00
 CL35 E:ENX1408 0.0 75.4 1.0
C13 E:ENX1408 1.7 73.0 1.0
C14 E:ENX1408 2.7 58.2 1.0
C12 E:ENX1408 2.7 81.0 1.0
C11 E:ENX1408 3.1 79.3 1.0
C15 E:ENX1408 3.1 52.0 1.0
CD2 E:LEU323 3.3 47.4 1.0
C34 E:ENX1408 3.4 77.8 1.0
CG E:LEU323 3.4 34.0 1.0
O33 E:ENX1408 3.4 76.7 1.0
CD1 E:LEU323 3.9 41.2 1.0
C16 E:ENX1408 4.5 53.1 1.0
O E:GLN125 4.5 53.0 1.0
C10 E:ENX1408 4.6 77.6 1.0
CD2 E:TYR321 4.6 48.2 1.0
CE2 E:TYR321 4.6 46.5 1.0
CB E:ALA397 4.7 82.9 1.0
CB E:LEU323 4.7 39.9 1.0
CA E:GLN125 4.8 56.4 1.0
OE2 E:GLU327 5.0 54.1 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: Sat Jul 20 00:52:15 2024

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