Magnesium in PDB 5c0w: Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates

The structure of Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates, PDB code: 5c0w 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)	59.09 / 4.60
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	195.380, 195.380, 463.650, 90.00, 90.00, 120.00
R / Rfree (%)	27.1 / 28.4

The structure of Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

The binding sites of Magnesium atom in the Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates (pdb code 5c0w). 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 Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates, PDB code: 5c0w:

Magnesium binding site 1 out of 1 in the Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A 12-Subunit Nuclear Exosome Complex Bound to Single- Stranded Rna Substrates within 5.0Å range: probe atom residue distance (Å) B Occ J:Mg1101 b:0.7 occ:1.00 OP1 R:A-1 1.9 0.0 1.0 OD1 J:ASP543 2.3 0.9 1.0 O3' R:A-2 2.4 0.5 1.0 P R:A-1 2.6 0.1 1.0 CG J:ASP543 3.2 1.0 1.0 OD2 J:ASP543 3.3 0.6 1.0 OD1 J:ASP552 3.4 0.8 1.0 O5' R:A-1 3.5 0.0 1.0 OD2 J:ASP552 3.5 0.4 1.0 CG J:ASP552 3.6 0.6 1.0 N J:ASP552 3.7 0.5 1.0 C3' R:A-2 3.8 0.9 1.0 O2' R:A-2 3.9 0.6 1.0 OP2 R:A-1 3.9 0.4 1.0 N J:ASN551 3.9 0.5 1.0 O J:ASP552 4.0 0.1 1.0 O J:ILE542 4.2 0.6 1.0 C4' R:A-2 4.3 0.5 1.0 CG2 J:ILE550 4.3 0.9 1.0 CB J:ASN551 4.4 0.8 1.0 C2' R:A-2 4.4 0.7 1.0 CA J:ASN551 4.4 0.5 1.0 CA J:ASP552 4.5 0.7 1.0 CB J:ASP543 4.5 0.2 1.0 C J:ASN551 4.6 0.6 1.0 CB J:ASP552 4.7 0.9 1.0 C J:ASP552 4.7 0.9 1.0 C J:ILE550 4.7 0.5 1.0 CA J:ILE550 4.8 0.8 1.0 C J:ILE542 4.8 0.8 1.0 C5' R:A-1 4.9 0.2 1.0 CA J:ASP543 4.9 0.8 1.0

D.L.Makino, B.Schuch, E.Stegmann, M.Baumgartner, C.Basquin, E.Conti. Rna Degradation Paths in A 12-Subunit Nuclear Exosome Complex. Nature V. 524 54 2015.
ISSN: ESSN 1476-4687
PubMed: 26222026
DOI: 10.1038/NATURE14865