Manganese in PDB 5izm: The Crystal Structure of Human Eefsec in Complex with Gdpnp

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

Resolution Low / High (Å)	46.16 / 3.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	92.316, 112.398, 327.669, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 28.5

The binding sites of Manganese atom in the The Crystal Structure of Human Eefsec in Complex with Gdpnp (pdb code 5izm). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the The Crystal Structure of Human Eefsec in Complex with Gdpnp, PDB code: 5izm:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in the The Crystal Structure of Human Eefsec in Complex with Gdpnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of The Crystal Structure of Human Eefsec in Complex with Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn1001 b:16.8 occ:1.00 O1B A:GNP1002 1.6 42.5 1.0 OG1 A:THR21 1.9 20.2 1.0 OG1 A:THR48 2.1 35.7 1.0 O3G A:GNP1002 2.2 55.5 1.0 CB A:THR48 2.6 32.2 1.0 PG A:GNP1002 3.0 96.2 1.0 CG2 A:THR48 3.0 22.9 1.0 PB A:GNP1002 3.0 37.6 1.0 CB A:THR21 3.2 13.4 1.0 N3B A:GNP1002 3.3 17.8 1.0 O1G A:GNP1002 3.4 66.0 1.0 OD1 A:ASP92 3.7 17.2 1.0 N A:THR21 3.8 14.6 1.0 O2B A:GNP1002 3.9 29.6 1.0 CA A:THR21 4.0 10.0 1.0 CA A:THR48 4.1 30.2 1.0 O3A A:GNP1002 4.1 66.5 1.0 OD2 A:ASP92 4.1 18.7 1.0 CG2 A:THR21 4.2 26.2 1.0 O A:CYS93 4.3 14.9 1.0 CG A:ASP92 4.3 19.3 1.0 CB A:LYS20 4.5 10.8 1.0 N A:THR48 4.5 39.2 1.0 O2G A:GNP1002 4.5 59.2 1.0 CE A:LYS20 4.8 17.9 1.0 O2A A:GNP1002 4.8 24.8 1.0 C A:ILE47 4.9 41.1 1.0 O A:THR48 4.9 20.3 1.0 C A:LYS20 4.9 12.3 1.0 O A:ILE47 4.9 41.5 1.0 PA A:GNP1002 5.0 58.7 1.0

Manganese binding site 2 out of 2 in the The Crystal Structure of Human Eefsec in Complex with Gdpnp


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of The Crystal Structure of Human Eefsec in Complex with Gdpnp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn1001 b:15.3 occ:1.00 O1B B:GNP1002 1.7 42.5 1.0 OG1 B:THR48 2.1 35.9 1.0 OG1 B:THR21 2.3 29.9 1.0 O3G B:GNP1002 2.6 55.5 1.0 CB B:THR21 3.1 30.4 1.0 O1G B:GNP1002 3.2 35.7 1.0 PG B:GNP1002 3.3 96.2 1.0 PB B:GNP1002 3.3 31.4 1.0 CB B:THR48 3.4 38.6 1.0 N3B B:GNP1002 3.8 50.4 1.0 O3A B:GNP1002 3.9 66.5 1.0 N B:THR21 3.9 27.4 1.0 N B:THR48 4.0 34.2 1.0 CG2 B:THR21 4.1 52.2 1.0 CA B:THR21 4.1 23.3 1.0 O1A B:GNP1002 4.3 24.8 1.0 CG2 B:THR48 4.3 38.2 1.0 O2B B:GNP1002 4.3 42.7 1.0 CA B:THR48 4.3 29.7 1.0 PA B:GNP1002 4.6 58.7 1.0 O B:CYS93 4.6 16.6 1.0 O2G B:GNP1002 4.8 59.2 1.0 O B:GLY46 4.8 38.5 1.0 C B:ILE47 5.0 30.1 1.0 CE B:LYS20 5.0 44.1 1.0 CB B:LYS20 5.0 24.5 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