Magnesium in PDB 5izl: The Crystal Structure of Human Eefsec in Complex with Gdpcp

The structure of The Crystal Structure of Human Eefsec in Complex with Gdpcp, PDB code: 5izl was solved by M.Dobosz-Bartoszek, M.Simonovic, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.77 / 2.72
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	94.302, 113.242, 329.725, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 28.6

The binding sites of Magnesium atom in the The Crystal Structure of Human Eefsec in Complex with Gdpcp (pdb code 5izl). 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 Crystal Structure of Human Eefsec in Complex with Gdpcp, PDB code: 5izl:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the The Crystal Structure of Human Eefsec in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The Crystal Structure of Human Eefsec in Complex with Gdpcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1001 b:65.0 occ:1.00 O1G A:GCP1002 1.9 70.3 1.0 OG1 A:THR48 2.0 78.1 1.0 O A:HOH1105 2.0 80.5 1.0 OG1 A:THR21 2.0 61.2 1.0 O A:HOH1104 2.2 0.9 1.0 O1B A:GCP1002 2.3 70.0 1.0 CB A:THR48 2.9 61.7 1.0 CB A:THR21 3.3 60.8 1.0 PG A:GCP1002 3.3 66.5 1.0 PB A:GCP1002 3.5 58.5 1.0 O3A A:GCP1002 3.8 83.5 1.0 OD2 A:ASP92 3.8 69.5 1.0 CG2 A:THR48 3.9 65.1 1.0 N A:THR21 3.9 61.5 1.0 OD1 A:ASP92 4.0 73.2 1.0 N A:THR48 4.0 59.9 1.0 O2G A:GCP1002 4.0 85.7 1.0 CA A:THR48 4.0 57.2 1.0 C3B A:GCP1002 4.0 73.7 1.0 CA A:THR21 4.1 59.5 1.0 CG2 A:THR21 4.3 57.0 1.0 O A:CYS93 4.3 60.3 1.0 CG A:ASP92 4.3 70.0 1.0 O3G A:GCP1002 4.4 84.0 1.0 CE A:LYS20 4.6 64.4 1.0 CB A:LYS20 4.7 58.5 1.0 O2B A:GCP1002 4.8 83.7 1.0 C A:LYS20 4.8 58.9 1.0 C A:ILE47 4.8 63.3 1.0 O2A A:GCP1002 4.9 63.2 1.0 PA A:GCP1002 4.9 67.8 1.0 O A:GLY46 5.0 88.2 1.0 NZ A:LYS20 5.0 71.5 1.0

Magnesium binding site 2 out of 2 in the The Crystal Structure of Human Eefsec in Complex with Gdpcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The Crystal Structure of Human Eefsec in Complex with Gdpcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1001 b:75.2 occ:1.00 OG1 B:THR48 2.2 68.8 1.0 O1B B:GCP1002 2.3 65.6 1.0 OG1 B:THR21 2.3 57.7 1.0 O3G B:GCP1002 2.6 63.6 1.0 O1G B:GCP1002 2.7 97.9 1.0 O B:HOH1106 2.7 82.8 1.0 PG B:GCP1002 2.9 52.8 1.0 CB B:THR48 3.2 59.3 1.0 CB B:THR21 3.3 56.7 1.0 PB B:GCP1002 3.3 55.5 1.0 O3A B:GCP1002 3.4 85.8 1.0 N B:THR48 3.6 68.2 1.0 O B:GLY46 3.7 88.7 1.0 C3B B:GCP1002 3.7 66.6 1.0 CA B:THR48 3.9 64.0 1.0 N B:THR21 4.2 58.0 1.0 CG2 B:THR21 4.2 62.8 1.0 CA B:THR21 4.4 59.0 1.0 CG2 B:THR48 4.4 59.5 1.0 C B:ILE47 4.4 65.1 1.0 PA B:GCP1002 4.4 56.3 1.0 O2A B:GCP1002 4.4 53.7 1.0 O2G B:GCP1002 4.5 68.0 1.0 OD2 B:ASP92 4.5 58.5 1.0 O2B B:GCP1002 4.7 89.4 1.0 CA B:ILE47 4.7 63.9 1.0 C B:GLY46 4.7 75.3 1.0 O1A B:GCP1002 4.8 0.9 1.0

M.Dobosz-Bartoszek, M.H.Pinkerton, Z.Otwinowski, S.Chakravarthy, D.Soll, P.R.Copeland, M.Simonovic. Crystal Structures of the Human Elongation Factor Eefsec Suggest A Non-Canonical Mechanism For Selenocysteine Incorporation. Nat Commun V. 7 12941 2016.
ISSN: ESSN 2041-1723
PubMed: 27708257
DOI: 10.1038/NCOMMS12941