Magnesium in PDB 6eze: The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp.

The structure of The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp., PDB code: 6eze was solved by J.S.Johansen, M.Blaise, S.S.Thirup, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.70 / 2.47
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.243, 243.589, 67.128, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 21.2

The binding sites of Magnesium atom in the The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp. (pdb code 6eze). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp., PDB code: 6eze:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:24.8 occ:1.00 O3G A:GNP401 2.0 25.0 1.0 OG1 A:THR25 2.0 20.7 1.0 O A:HOH517 2.0 23.1 1.0 O2B A:GNP401 2.1 19.3 1.0 O A:HOH515 2.1 22.1 1.0 O A:HOH511 2.2 23.7 1.0 CB A:THR25 3.2 26.2 1.0 PG A:GNP401 3.2 29.4 1.0 PB A:GNP401 3.2 22.1 1.0 N3B A:GNP401 3.4 25.5 1.0 N A:THR25 3.7 21.0 1.0 O A:CYS81 3.9 39.1 1.0 CA A:THR25 4.0 21.6 1.0 O1A A:GNP401 4.0 22.3 1.0 OD1 A:ASP80 4.0 30.9 1.0 O1G A:GNP401 4.1 35.5 1.0 OD1 A:ASP50 4.1 38.0 1.0 O1B A:GNP401 4.2 25.1 1.0 O2G A:GNP401 4.2 25.5 1.0 O A:HOH506 4.2 23.9 1.0 CG2 A:THR25 4.3 21.6 1.0 O3A A:GNP401 4.3 30.1 1.0 O A:HOH603 4.5 40.9 1.0 PA A:GNP401 4.5 20.8 1.0 OD2 A:ASP80 4.5 31.4 1.0 O2A A:GNP401 4.6 26.8 1.0 CA A:PRO82 4.6 38.2 1.0 CB A:LYS24 4.6 21.8 1.0 CE A:LYS24 4.6 22.0 1.0 CG A:ASP80 4.7 28.8 1.0 C A:LYS24 4.8 24.7 1.0 C A:CYS81 4.8 36.4 1.0 NZ A:LYS24 4.8 18.7 1.0

Magnesium binding site 2 out of 2 in the The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp.


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Open Conformation of E.Coli Elongation Factor Tu in Complex with Gdpnp. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:33.4 occ:1.00 O3G B:GNP401 2.0 31.9 1.0 OG1 B:THR25 2.0 41.0 1.0 O B:HOH528 2.0 29.7 1.0 O1B B:GNP401 2.1 26.9 1.0 O B:HOH555 2.2 31.5 1.0 O B:HOH510 2.2 26.0 1.0 CB B:THR25 3.1 37.1 1.0 PB B:GNP401 3.2 29.4 1.0 PG B:GNP401 3.2 40.2 1.0 N3B B:GNP401 3.4 39.2 1.0 N B:THR25 3.7 31.2 1.0 O B:CYS81 4.0 35.3 1.0 OD1 B:ASP50 4.0 46.2 1.0 OD1 B:ASP80 4.0 36.5 1.0 CA B:THR25 4.0 33.3 1.0 O1A B:GNP401 4.0 33.6 1.0 O1G B:GNP401 4.1 40.9 1.0 O2B B:GNP401 4.1 23.5 1.0 O2G B:GNP401 4.2 31.8 1.0 CG2 B:THR25 4.2 39.8 1.0 O B:HOH574 4.2 39.5 1.0 O B:HOH554 4.3 31.4 1.0 O3A B:GNP401 4.3 34.4 1.0 OD2 B:ASP80 4.5 31.7 1.0 PA B:GNP401 4.5 36.5 1.0 CA B:PRO82 4.6 36.9 1.0 O2A B:GNP401 4.6 33.6 1.0 CG B:ASP80 4.7 34.4 1.0 CE B:LYS24 4.7 25.4 1.0 CB B:LYS24 4.7 23.6 1.0 NZ B:LYS24 4.8 27.2 1.0 C B:LYS24 4.8 29.8 1.0 C B:CYS81 4.8 35.3 1.0

J.S.Johansen, D.Kavaliauskas, S.H.Pfeil, M.Blaise, B.S.Cooperman, Y.E.Goldman, S.S.Thirup, C.R.Knudsen. E. Coli Elongation Factor Tu Bound to A Gtp Analogue Displays An Open Conformation Equivalent to the Gdp-Bound Form. Nucleic Acids Res. V. 46 8641 2018.
ISSN: ESSN 1362-4962
PubMed: 30107565
DOI: 10.1093/NAR/GKY697