Magnesium in PDB 4ifd: Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd was solved by D.L.Makino, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.64 / 2.81
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	154.090, 107.440, 150.460, 90.00, 110.63, 90.00
R / Rfree (%)	18.3 / 22.4

The structure of Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna also contains other interesting chemical elements:

Bromine	(Br)	10 atoms
Zinc	(Zn)	1 atom

The binding sites of Magnesium atom in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna (pdb code 4ifd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna, PDB code: 4ifd:

Magnesium binding site 1 out of 1 in the Crystal Structure of An 11-Subunit Eukaryotic Exosome Complex Bound to Rna


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 An 11-Subunit Eukaryotic Exosome Complex Bound to Rna within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1105 b:72.4 occ:1.00 O3' R:U-2 2.1 92.7 1.0 OD1 J:ASP552 2.1 0.2 1.0 OD1 J:ASP543 2.1 0.8 1.0 OD2 J:ASP552 2.2 0.2 1.0 CG J:ASP552 2.4 0.0 1.0 OP1 R:U-1 2.4 76.7 1.0 P R:U-1 2.8 72.6 1.0 CG J:ASP543 3.1 0.2 1.0 C3' R:U-2 3.3 89.4 1.0 OD2 J:ASP543 3.5 0.2 1.0 N J:ASP552 3.5 86.3 1.0 C4' R:U-2 3.7 86.6 1.0 CB J:ASP552 3.7 98.3 1.0 O5' R:U-1 3.9 0.2 1.0 O2' R:U-2 3.9 90.4 1.0 OP2 R:U-1 3.9 65.2 1.0 CA J:ASP552 4.1 90.8 1.0 C5' R:U-2 4.1 81.0 1.0 N J:ASN551 4.1 76.7 1.0 O J:ASP552 4.2 94.8 1.0 C2' R:U-2 4.2 90.3 1.0 O J:ILE542 4.5 0.3 1.0 C J:ASP552 4.5 91.1 1.0 CB J:ASP543 4.5 0.5 1.0 C J:ASN551 4.6 80.7 1.0 CB J:ASN551 4.7 82.4 1.0 CA J:ASN551 4.7 79.5 1.0 CG2 J:ILE550 4.8 75.9 1.0 O5' R:U-2 5.0 77.0 1.0 O4' R:U-2 5.0 86.9 1.0

D.L.Makino, M.Baumgartner, E.Conti. Crystal Structure of An Rna-Bound 11-Subunit Eukaryotic Exosome Complex. Nature V. 495 70 2013.
ISSN: ISSN 0028-0836
PubMed: 23376952
DOI: 10.1038/NATURE11870