Magnesium in PDB 1ttt: Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex

The structure of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex, PDB code: 1ttt was solved by P.Nissen, M.Kjeldgaard, S.Thirup, G.Polekhina, L.Reshetnikova, B.F.C.Clark, J.Nyborg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	206.835, 122.354, 151.552, 90.00, 126.30, 90.00
R / Rfree (%)	20.6 / 29.6

The binding sites of Magnesium atom in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex (pdb code 1ttt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex, PDB code: 1ttt:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg78 b:23.4 occ:1.00 N4 D:C63 4.1 29.3 0.7 N6 D:A64 4.2 26.5 0.9 O4 D:U50 4.9 31.3 0.9 C5 D:C63 5.0 30.5 0.8 C4 D:C63 5.0 32.2 0.7

Magnesium binding site 2 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:Mg78 b:38.9 occ:1.00 N4 E:C63 3.8 39.3 0.6 N6 E:A64 4.1 20.8 0.9 C5 E:C63 4.5 31.4 0.9 C4 E:C63 4.6 35.1 0.9

Magnesium binding site 3 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg78 b:39.1 occ:1.00 N4 F:C63 3.8 27.6 0.8 N6 F:A64 4.1 30.7 0.9 C5 F:C63 4.8 19.2 0.9 C4 F:C63 4.8 23.9 0.6 O4 F:U50 4.9 37.7 1.0

Magnesium binding site 4 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg407 b:31.2 occ:1.00 OG1 A:THR62 2.1 40.2 1.0 O2B A:GNP406 2.2 28.7 1.0 O3G A:GNP406 2.5 25.8 1.0 OG1 A:THR25 2.5 46.4 0.9 O A:HOH410 2.8 29.2 1.0 OD2 A:ASP51 2.8 40.1 1.0 O1A A:GNP406 3.0 41.6 1.0 CB A:THR62 3.2 43.6 1.0 PG A:GNP406 3.2 45.4 1.0 PB A:GNP406 3.2 43.2 1.0 N3B A:GNP406 3.2 43.9 1.0 CB A:THR25 3.4 44.0 0.9 O1G A:GNP406 3.5 52.0 1.0 N A:THR62 3.5 44.3 1.0 O3A A:GNP406 3.8 54.7 0.9 CG A:ASP51 3.8 46.0 0.6 CA A:THR62 3.9 42.5 1.0 PA A:GNP406 4.0 48.0 0.9 OD1 A:ASP51 4.2 51.3 0.8 C A:ILE61 4.3 48.7 1.0 OH A:TYR47 4.3 66.0 0.6 CG2 A:THR25 4.3 40.7 0.8 N A:THR25 4.4 39.5 1.0 CG2 A:THR62 4.5 42.0 0.9 CA A:THR25 4.6 42.4 1.0 O1B A:GNP406 4.6 42.6 1.0 O2A A:GNP406 4.6 38.3 1.0 CA A:ILE61 4.6 49.2 1.0 O2G A:GNP406 4.7 42.6 1.0 CZ A:TYR47 4.9 60.2 1.0 OD2 A:ASP81 5.0 41.5 0.9

Magnesium binding site 5 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg407 b:29.0 occ:1.00 OG1 B:THR25 2.1 51.3 1.0 OG1 B:THR62 2.2 36.1 1.0 O2B B:GNP406 2.3 36.2 1.0 O B:HOH409 2.4 12.3 1.0 O3G B:GNP406 2.5 31.8 1.0 CB B:THR25 3.0 47.4 1.0 OD2 B:ASP51 3.1 49.1 0.9 O1A B:GNP406 3.2 49.9 0.9 PG B:GNP406 3.2 46.3 0.9 PB B:GNP406 3.3 47.6 1.0 CB B:THR62 3.3 39.8 1.0 O1G B:GNP406 3.4 46.0 1.0 N3B B:GNP406 3.4 51.0 1.0 N B:THR62 3.8 49.3 1.0 N B:THR25 3.9 40.0 1.0 CG B:ASP51 4.0 48.0 0.9 OD1 B:ASP51 4.0 54.4 0.7 CA B:THR25 4.0 44.5 1.0 O3A B:GNP406 4.0 42.0 1.0 PA B:GNP406 4.1 43.9 0.9 CG2 B:THR25 4.1 42.2 1.0 CA B:THR62 4.1 48.3 1.0 OH B:TYR47 4.4 78.3 0.5 CG2 B:THR62 4.5 38.0 1.0 OD2 B:ASP81 4.5 42.1 1.0 O1B B:GNP406 4.5 52.1 1.0 O2A B:GNP406 4.6 33.7 1.0 O2G B:GNP406 4.7 47.5 1.0 C B:ILE61 4.8 50.4 0.9 CA B:ILE61 5.0 52.4 0.9

Magnesium binding site 6 out of 6 in the Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Phe-Trna, Elongation Factor Ef-Tu:Gdpnp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg407 b:41.9 occ:1.00 OG1 C:THR62 2.3 61.4 1.0 O2B C:GNP406 2.4 71.7 1.0 OG1 C:THR25 2.4 51.1 1.0 O3G C:GNP406 2.6 69.7 0.9 O1A C:GNP406 2.7 63.8 1.0 OD2 C:ASP51 2.9 52.8 1.0 CB C:THR25 3.1 42.9 0.6 O1G C:GNP406 3.1 52.6 1.0 OD1 C:ASP51 3.2 51.1 1.0 PG C:GNP406 3.2 65.0 0.9 CB C:THR62 3.4 62.1 0.6 N3B C:GNP406 3.5 71.6 0.9 CG C:ASP51 3.5 52.4 0.5 PB C:GNP406 3.6 70.9 0.9 OH C:TYR47 3.6 52.1 1.0 N C:THR62 3.6 67.5 0.9 CG2 C:THR25 3.8 29.0 1.0 PA C:GNP406 3.9 72.7 0.9 CA C:THR62 4.0 63.1 0.7 O3A C:GNP406 4.1 72.4 0.9 CZ C:TYR47 4.2 46.2 0.8 C C:ILE61 4.4 67.0 0.9 CA C:THR25 4.4 43.0 1.0 N C:THR25 4.5 37.0 1.0 O2A C:GNP406 4.5 73.3 1.0 CA C:ILE61 4.6 70.0 0.9 O2G C:GNP406 4.7 54.5 1.0 CG2 C:THR62 4.7 60.4 0.8 CE1 C:TYR47 4.8 44.2 0.7 CE2 C:TYR47 4.9 43.8 0.7 O1B C:GNP406 4.9 63.9 1.0

P.Nissen, M.Kjeldgaard, S.Thirup, G.Polekhina, L.Reshetnikova, B.F.Clark, J.Nyborg. Crystal Structure of the Ternary Complex of Phe-Trnaphe, Ef-Tu, and A Gtp Analog. Science V. 270 1464 1995.
ISSN: ISSN 0036-8075
PubMed: 7491491