Magnesium in PDB 1b23: E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex

The structure of E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex, PDB code: 1b23 was solved by P.Nissen, M.Kjeldgaard, S.Thirup, J.Nyborg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.60
Space group	F 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	126.750, 132.980, 154.880, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 26.3

The binding sites of Magnesium atom in the E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex (pdb code 1b23). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex, PDB code: 1b23:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg77 b:55.6 occ:1.00 OP2 R:A76 1.6 79.7 1.0 P R:A76 2.9 80.9 1.0 C8 R:A76 3.0 52.6 1.0 O5' R:A76 3.1 80.3 1.0 O2' R:C75 3.5 88.5 1.0 N7 R:A76 3.6 52.6 1.0 O R:HOH983 3.8 68.6 1.0 O3' R:C75 3.9 81.8 1.0 OP1 R:A76 3.9 79.8 1.0 N9 R:A76 4.1 52.0 1.0 CG P:ARG274 4.3 58.6 1.0 C5' R:A76 4.3 72.5 1.0 C2' R:A76 4.5 59.1 1.0 CD1 P:ILE231 4.5 69.6 1.0 O4' R:A76 4.5 59.5 1.0 C1' R:A76 4.6 56.2 1.0 CD P:ARG274 4.7 65.0 1.0 C2' R:C75 4.7 86.3 1.0 C4' R:A76 4.9 65.9 1.0 C5 R:A76 4.9 51.5 1.0 O2 R:C75 5.0 83.1 1.0

Magnesium binding site 2 out of 3 in the E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ R:Mg179 b:54.9 occ:0.50 O2' R:G70 3.4 77.2 1.0 C1' R:G70 3.9 79.2 1.0 N2 R:G4 4.0 80.5 1.0 C2' R:G70 4.2 76.8 1.0 O R:HOH1034 4.3 35.8 1.0 N3 R:G70 4.6 82.2 1.0 O4' R:G70 4.7 76.8 1.0 N9 R:G70 4.9 81.0 1.0

Magnesium binding site 3 out of 3 in the E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of E. Coli Cysteinyl-Trna and T. Aquaticus Elongation Factor Ef-Tu:Gtp Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Mg407 b:26.9 occ:1.00 O P:HOH410 1.9 30.5 1.0 O2B P:GNP406 2.0 38.6 1.0 O3G P:GNP406 2.1 35.2 1.0 OG1 P:THR25 2.1 32.4 1.0 OG1 P:THR62 2.3 58.6 1.0 O P:HOH419 2.6 28.2 1.0 CB P:THR62 3.1 58.9 1.0 PB P:GNP406 3.1 43.8 1.0 N3B P:GNP406 3.1 41.8 1.0 PG P:GNP406 3.2 39.1 1.0 CB P:THR25 3.4 29.2 1.0 N P:THR25 3.7 28.8 1.0 OD2 P:ASP81 3.8 41.4 1.0 CG2 P:THR62 3.9 60.1 1.0 O1B P:GNP406 4.0 34.6 1.0 CA P:THR25 4.1 29.5 1.0 O2G P:GNP406 4.2 30.8 1.0 CE P:LYS24 4.2 30.4 1.0 O2A P:GNP406 4.2 45.6 1.0 O P:CYS82 4.2 41.1 1.0 CB P:LYS24 4.2 30.3 1.0 O1G P:GNP406 4.2 37.4 1.0 CA P:THR62 4.3 58.3 1.0 N P:THR62 4.3 57.9 1.0 OD2 P:ASP51 4.5 31.3 1.0 OD1 P:ASP81 4.5 38.0 1.0 CG2 P:THR25 4.5 18.2 1.0 CG P:ASP81 4.6 38.7 1.0 C P:LYS24 4.6 28.0 1.0 O1A P:GNP406 4.7 34.9 1.0 OD1 P:ASP51 4.7 40.8 1.0 PA P:GNP406 4.8 42.3 1.0 CA P:LYS24 4.9 30.1 1.0 O3A P:GNP406 4.9 40.8 1.0 NZ P:LYS24 4.9 31.4 1.0

P.Nissen, S.Thirup, M.Kjeldgaard, J.Nyborg. The Crystal Structure of Cys-Trnacys-Ef-Tu-Gdpnp Reveals General and Specific Features in the Ternary Complex and in Trna. Structure Fold.Des. V. 7 143 1999.
ISSN: ISSN 0969-2126
PubMed: 10368282
DOI: 10.1016/S0969-2126(99)80021-5