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Chlorine in PDB 2bvn: E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia

Enzymatic activity of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia

All present enzymatic activity of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia:
3.6.1.48;

Protein crystallography data

The structure of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia, PDB code: 2bvn was solved by A.Parmeggiani, I.M.Krab, T.Watanabe, R.C.Nielsen, C.Dahlberg, J.Nyborg, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.06 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.070, 72.070, 335.730, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27.1

Other elements in 2bvn:

The structure of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia (pdb code 2bvn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia, PDB code: 2bvn:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 2bvn

Go back to Chlorine Binding Sites List in 2bvn
Chlorine binding site 1 out of 4 in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1396

b:19.2
occ:1.00
 CL30 A:ENX1396 0.0 19.2 1.0
C6 A:ENX1396 1.8 41.9 1.0
C5 A:ENX1396 2.7 48.7 1.0
C7 A:ENX1396 2.7 42.8 1.0
O31 A:ENX1396 3.1 54.6 1.0
C4 A:ENX1396 3.1 47.0 1.0
O A:PHE374 3.2 37.7 1.0
C8 A:ENX1396 3.2 44.4 1.0
C A:PHE374 3.5 33.4 1.0
O A:HOH2081 3.5 39.9 1.0
CB A:ALA375 3.6 36.5 1.0
CA A:ALA375 3.7 40.1 1.0
N A:ALA375 3.8 40.6 1.0
CB A:ALA385 3.9 31.0 1.0
O29 A:ENX1396 4.0 57.2 1.0
CA A:ALA385 4.1 41.4 1.0
C3 A:ENX1396 4.2 46.7 1.0
N A:PHE374 4.4 36.4 1.0
CA A:PHE374 4.4 34.3 1.0
C9 A:ENX1396 4.6 49.4 1.0
N A:GLY386 4.6 43.2 1.0
C A:ALA385 4.8 44.2 1.0
O A:GLY386 4.9 42.7 1.0
O A:GLN124 5.0 42.6 1.0
O A:GLY384 5.0 40.5 1.0

Chlorine binding site 2 out of 4 in 2bvn

Go back to Chlorine Binding Sites List in 2bvn
Chlorine binding site 2 out of 4 in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1396

b:26.4
occ:1.00
 CL35 A:ENX1396 0.0 26.4 1.0
C13 A:ENX1396 1.7 33.6 1.0
C14 A:ENX1396 2.7 36.2 1.0
C12 A:ENX1396 2.8 40.4 1.0
C15 A:ENX1396 3.1 34.9 1.0
C34 A:ENX1396 3.2 43.2 1.0
C11 A:ENX1396 3.2 42.4 1.0
CD1 A:LEU311 3.5 46.4 1.0
CD2 A:LEU311 3.6 37.5 1.0
O A:GLN124 3.7 42.6 1.0
O33 A:ENX1396 3.8 39.2 1.0
CA A:GLN124 4.0 31.6 1.0
CG A:LEU311 4.2 48.3 1.0
CB A:ALA385 4.2 31.0 1.0
CB A:GLN124 4.2 31.8 1.0
C A:GLN124 4.3 38.0 1.0
C16 A:ENX1396 4.5 40.8 1.0
CG A:GLN124 4.6 27.1 1.0
C10 A:ENX1396 4.7 46.9 1.0
CD1 A:TYR309 5.0 35.4 1.0

Chlorine binding site 3 out of 4 in 2bvn

Go back to Chlorine Binding Sites List in 2bvn
Chlorine binding site 3 out of 4 in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1396

b:8.9
occ:1.00
 CL30 B:ENX1396 0.0 8.9 1.0
C6 B:ENX1396 1.8 42.8 1.0
C5 B:ENX1396 2.7 47.6 1.0
C7 B:ENX1396 2.8 43.8 1.0
O31 B:ENX1396 3.1 44.9 1.0
C4 B:ENX1396 3.1 55.5 1.0
O B:PHE374 3.1 45.3 1.0
C8 B:ENX1396 3.2 52.0 1.0
C B:PHE374 3.5 38.0 1.0
O B:HOH2093 3.6 37.9 1.0
CB B:ALA375 3.6 24.9 1.0
CA B:ALA375 3.7 34.7 1.0
N B:ALA375 3.8 36.8 1.0
CB B:ALA385 3.9 27.7 1.0
O29 B:ENX1396 4.0 56.9 1.0
CA B:ALA385 4.1 37.6 1.0
C3 B:ENX1396 4.2 65.8 1.0
N B:PHE374 4.4 39.3 1.0
CA B:PHE374 4.4 39.0 1.0
C9 B:ENX1396 4.6 53.1 1.0
N B:GLY386 4.6 39.6 1.0
O B:GLY386 4.8 40.7 1.0
C B:ALA385 4.8 39.1 1.0

Chlorine binding site 4 out of 4 in 2bvn

Go back to Chlorine Binding Sites List in 2bvn
Chlorine binding site 4 out of 4 in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1396

b:28.0
occ:1.00
 CL35 B:ENX1396 0.0 28.0 1.0
C13 B:ENX1396 1.7 33.8 1.0
C14 B:ENX1396 2.7 28.0 1.0
C12 B:ENX1396 2.8 40.2 1.0
C15 B:ENX1396 3.1 35.8 1.0
C34 B:ENX1396 3.2 37.6 1.0
C11 B:ENX1396 3.3 43.7 1.0
CD1 B:LEU311 3.4 31.1 1.0
CD2 B:LEU311 3.6 38.9 1.0
O33 B:ENX1396 3.8 47.8 1.0
O B:GLN124 3.8 32.1 1.0
CA B:GLN124 4.1 34.3 1.0
CG B:LEU311 4.1 39.0 1.0
CB B:ALA385 4.3 27.7 1.0
CB B:GLN124 4.3 30.3 1.0
C B:GLN124 4.4 34.8 1.0
C16 B:ENX1396 4.5 33.2 1.0
CG B:GLN124 4.6 36.4 1.0
C10 B:ENX1396 4.7 49.6 1.0
CD1 B:TYR309 4.9 42.5 1.0
CE1 B:TYR309 5.0 43.1 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 05:56:03 2024

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