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Magnesium 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:

Chlorine (Cl) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the E. Coli Ef-Tu:Gdpnp in Complex with the Antibiotic Enacyloxin Iia, PDB code: 2bvn:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 2bvn

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg1395

b:36.2
occ:1.00
O1G A:GNP1394 1.9 27.3 1.0
O2B A:GNP1394 2.0 23.2 1.0
O A:HOH2004 2.1 31.7 1.0
O A:HOH2003 2.1 34.0 1.0
OG1 A:THR25 2.2 35.2 1.0
PB A:GNP1394 3.1 39.5 1.0
PG A:GNP1394 3.1 41.8 1.0
N3B A:GNP1394 3.2 40.0 1.0
CB A:THR25 3.4 44.9 1.0
O3G A:GNP1394 3.8 51.6 1.0
N A:THR25 3.9 39.0 1.0
O A:HOH2082 4.0 37.6 1.0
O2A A:GNP1394 4.1 35.6 1.0
O2G A:GNP1394 4.1 36.4 1.0
O3A A:GNP1394 4.1 41.1 1.0
O1B A:GNP1394 4.2 32.8 1.0
CA A:THR25 4.2 37.5 1.0
OD2 A:ASP80 4.3 45.2 1.0
CG2 A:THR25 4.4 42.1 1.0
PA A:GNP1394 4.5 43.4 1.0
CB A:LYS24 4.6 32.0 1.0
O A:CYS81 4.6 44.0 1.0
CE A:LYS24 4.6 39.1 1.0
OD1 A:ASP80 4.7 34.6 1.0
O1A A:GNP1394 4.8 42.9 1.0
CA A:PRO82 4.8 47.0 1.0
CG A:ASP80 4.9 39.0 1.0
C A:LYS24 5.0 32.1 1.0

Magnesium binding site 2 out of 2 in 2bvn

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


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg1395

b:34.0
occ:1.00
O B:HOH2005 2.0 30.5 1.0
O2B B:GNP1394 2.0 31.2 1.0
OG1 B:THR25 2.0 29.2 1.0
O1G B:GNP1394 2.1 32.8 1.0
O B:HOH2007 2.1 29.4 1.0
O B:HOH2006 2.2 31.5 1.0
PB B:GNP1394 3.2 35.3 1.0
CB B:THR25 3.2 36.5 1.0
PG B:GNP1394 3.3 40.5 1.0
N3B B:GNP1394 3.3 36.4 1.0
N B:THR25 3.8 34.5 1.0
O B:HOH2094 3.9 40.1 1.0
O3G B:GNP1394 4.0 50.1 1.0
CA B:THR25 4.1 29.5 1.0
OD2 B:ASP80 4.1 36.4 1.0
O2A B:GNP1394 4.2 36.0 1.0
O1B B:GNP1394 4.2 26.1 1.0
O3A B:GNP1394 4.3 37.8 1.0
O2G B:GNP1394 4.3 41.3 1.0
CG2 B:THR25 4.3 20.1 1.0
OD1 B:ASP80 4.5 30.9 1.0
CB B:LYS24 4.5 35.1 1.0
O B:CYS81 4.6 42.4 1.0
CE B:LYS24 4.6 31.5 1.0
PA B:GNP1394 4.6 36.6 1.0
CG B:ASP80 4.7 37.7 1.0
O1A B:GNP1394 4.8 38.7 1.0
C B:LYS24 4.8 31.5 1.0
CA B:PRO82 4.8 43.2 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: Mon Dec 14 07:17:44 2020

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