Magnesium in PDB 1d2e: Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp

The structure of Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp, PDB code: 1d2e was solved by G.R.Andersen, S.Thirup, L.L.Spremulli, J.Nyborg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.70 / 1.94
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.090, 119.780, 128.890, 90.00, 96.97, 90.00
R / Rfree (%)	23.7 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp (pdb code 1d2e). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp, PDB code: 1d2e:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg501 b:26.9 occ:1.00 O A:HOH1686 1.9 26.8 1.0 O2B A:GDP1301 2.0 18.9 1.0 OG1 A:THR71 2.0 21.9 1.0 O A:HOH1687 2.1 25.1 1.0 O A:HOH1685 2.1 26.5 1.0 O A:HOH1688 2.2 22.2 1.0 CB A:THR71 3.1 18.2 1.0 PB A:GDP1301 3.2 21.1 1.0 O3B A:GDP1301 3.4 19.8 1.0 N A:THR71 3.8 21.7 1.0 OD2 A:ASP126 3.9 27.9 1.0 CA A:THR71 4.0 21.6 1.0 O A:CYS127 4.0 28.9 1.0 O1A A:GDP1301 4.0 24.5 1.0 O A:HOH1311 4.1 25.9 1.0 CG2 A:THR71 4.2 24.5 1.0 OD1 A:ASP96 4.2 33.4 1.0 O3A A:GDP1301 4.2 24.2 1.0 O1B A:GDP1301 4.2 20.4 1.0 O A:HOH1361 4.2 35.4 1.0 O A:PRO128 4.3 31.8 1.0 OD1 A:ASP126 4.4 26.6 1.0 CA A:PRO128 4.4 31.3 1.0 PA A:GDP1301 4.5 28.2 1.0 CG A:ASP126 4.5 28.1 1.0 O A:HOH1336 4.6 28.3 1.0 CB A:LYS70 4.6 23.4 1.0 C A:CYS127 4.7 30.2 1.0 O2A A:GDP1301 4.7 26.2 1.0 C A:LYS70 4.8 22.8 1.0 CE A:LYS70 4.8 23.9 1.0 C A:PRO128 4.9 29.9 1.0 NZ A:LYS70 4.9 23.2 1.0 N A:PRO128 4.9 31.5 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg502 b:49.2 occ:1.00 OG1 B:THR71 1.9 42.7 1.0 O B:HOH1574 1.9 53.9 1.0 O B:HOH1573 2.0 48.0 1.0 O B:HOH1576 2.0 42.0 1.0 O2B B:GDP1302 2.1 44.4 1.0 O B:HOH1575 2.2 44.7 1.0 CB B:THR71 3.2 42.6 1.0 PB B:GDP1302 3.2 45.0 1.0 O3B B:GDP1302 3.3 47.0 1.0 OD2 B:ASP126 3.8 49.0 1.0 N B:THR71 3.9 41.2 1.0 OD1 B:ASP96 3.9 64.2 1.0 O B:CYS127 4.0 45.9 1.0 O1A B:GDP1302 4.1 46.5 1.0 CA B:THR71 4.1 41.7 1.0 CG2 B:THR71 4.1 42.8 1.0 O3A B:GDP1302 4.2 46.6 1.0 O B:PRO128 4.2 47.3 1.0 O1B B:GDP1302 4.3 45.1 1.0 CA B:PRO128 4.4 47.8 1.0 O B:HOH1475 4.4 50.3 1.0 PA B:GDP1302 4.5 47.9 1.0 OD1 B:ASP126 4.6 48.2 1.0 CG B:ASP126 4.6 48.4 1.0 O2A B:GDP1302 4.7 47.7 1.0 C B:CYS127 4.7 47.0 1.0 C B:PRO128 4.8 47.4 1.0 CB B:LYS70 4.8 39.5 1.0 N B:PRO128 4.9 47.3 1.0 C B:LYS70 5.0 41.5 1.0 CE B:LYS70 5.0 34.3 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg503 b:35.9 occ:1.00 OG1 C:THR71 1.9 33.5 1.0 O C:HOH1597 2.0 32.3 1.0 O2B C:GDP1303 2.0 32.4 1.0 O C:HOH1595 2.1 37.6 1.0 O C:HOH1596 2.2 40.1 1.0 O C:HOH1598 2.3 37.0 1.0 CB C:THR71 3.1 30.3 1.0 PB C:GDP1303 3.3 32.8 1.0 O3B C:GDP1303 3.6 34.4 1.0 N C:THR71 3.7 30.5 1.0 OD2 C:ASP126 3.7 38.5 1.0 CA C:THR71 3.9 31.3 1.0 O C:CYS127 4.0 41.7 1.0 O1A C:GDP1303 4.1 39.7 1.0 CG2 C:THR71 4.2 31.2 1.0 OD1 C:ASP96 4.2 53.0 1.0 O C:HOH1335 4.2 48.9 1.0 O1B C:GDP1303 4.3 34.7 1.0 OD1 C:ASP126 4.3 38.9 1.0 O3A C:GDP1303 4.3 35.2 1.0 CA C:PRO128 4.4 43.4 1.0 CG C:ASP126 4.4 37.8 1.0 O C:PRO128 4.4 42.0 1.0 CB C:LYS70 4.5 29.6 1.0 PA C:GDP1303 4.6 37.4 1.0 O2A C:GDP1303 4.6 37.5 1.0 C C:CYS127 4.6 42.5 1.0 C C:LYS70 4.7 31.2 1.0 CE C:LYS70 4.8 29.1 1.0 N C:PRO128 4.8 43.3 1.0 NZ C:LYS70 4.9 28.0 1.0 O C:HOH1517 4.9 49.9 1.0 C C:PRO128 4.9 41.9 1.0 O C:HOH1323 5.0 35.7 1.0 O C:HOH1346 5.0 61.7 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mitochondrial Ef-Tu in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg504 b:52.6 occ:1.00 O D:HOH1548 1.9 46.6 1.0 O D:HOH1549 1.9 45.8 1.0 O2B D:GDP1304 2.1 58.6 1.0 OG1 D:THR71 2.3 51.0 1.0 O3B D:GDP1304 2.8 55.8 1.0 PB D:GDP1304 3.0 56.8 1.0 CB D:THR71 3.5 51.6 1.0 O D:PRO128 3.9 60.8 1.0 N D:THR71 4.0 50.5 1.0 O D:CYS127 4.0 59.8 1.0 O1B D:GDP1304 4.1 57.6 1.0 O3A D:GDP1304 4.1 58.3 1.0 O1A D:GDP1304 4.1 58.1 1.0 OD2 D:ASP126 4.1 56.6 1.0 CA D:PRO128 4.1 60.4 1.0 CA D:THR71 4.3 51.5 1.0 OD1 D:ASP96 4.4 66.2 1.0 OD1 D:ASP126 4.4 57.5 1.0 C D:PRO128 4.5 60.3 1.0 PA D:GDP1304 4.6 57.8 1.0 NZ D:LYS70 4.6 43.5 1.0 O D:HOH1353 4.6 47.1 1.0 CG2 D:THR71 4.6 52.8 1.0 CB D:LYS70 4.7 46.7 1.0 C D:CYS127 4.7 59.5 1.0 CG D:ASP126 4.7 58.4 1.0 CE D:LYS70 4.7 41.8 1.0 N D:PRO128 4.8 60.3 1.0 O2A D:GDP1304 4.8 54.5 1.0

G.R.Andersen, S.Thirup, L.L.Spremulli, J.Nyborg. High Resolution Crystal Structure of Bovine Mitochondrial Ef-Tu in Complex with Gdp. J.Mol.Biol. V. 297 421 2000.
ISSN: ISSN 0022-2836
PubMed: 10715211
DOI: 10.1006/JMBI.2000.3564