Magnesium in PDB 5c0y: Crystal Structure of the RRP6 Catalytic Domain Bound to Poly(U) Rna

The structure of Crystal Structure of the RRP6 Catalytic Domain Bound to Poly(U) Rna, PDB code: 5c0y was solved by B.Schuch, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.71 / 2.10
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	110.186, 110.186, 78.883, 90.00, 90.00, 120.00
R / Rfree (%)	14.8 / 18

The binding sites of Magnesium atom in the Crystal Structure of the RRP6 Catalytic Domain Bound to Poly(U) Rna (pdb code 5c0y). 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 the RRP6 Catalytic Domain Bound to Poly(U) Rna, PDB code: 5c0y:

Magnesium binding site 1 out of 1 in the Crystal Structure of the RRP6 Catalytic Domain Bound to Poly(U) 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 the RRP6 Catalytic Domain Bound to Poly(U) Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:55.5 occ:1.00 OD2 B:ASP238 2.5 36.4 1.0 OD2 B:ASP365 2.5 46.5 1.0 OE2 B:GLU240 2.6 61.9 1.0 OD1 B:ASP238 2.6 30.8 1.0 CG B:ASP238 2.6 34.8 1.0 O5' D:U15 2.7 83.9 0.8 O B:LEU239 2.8 45.5 1.0 C5' D:U15 3.0 73.9 0.8 CG B:ASP365 3.4 38.3 1.0 C4' D:U15 3.5 76.1 0.8 CD B:GLU240 3.5 54.9 1.0 NE2 B:GLN255 3.6 41.0 1.0 C B:LEU239 3.8 37.9 1.0 CB B:ASP238 3.8 32.5 1.0 OP1 D:U15 4.0 87.3 0.8 O D:HOH111 4.0 46.2 1.0 P D:U15 4.0 90.7 0.8 N B:LEU239 4.1 35.3 1.0 OD1 B:ASP365 4.1 40.4 1.0 OE1 B:GLU240 4.1 51.0 1.0 CB B:ASP365 4.2 37.0 1.0 O4' D:U15 4.4 83.2 0.8 O D:HOH105 4.4 36.1 1.0 CG B:GLU240 4.6 48.3 1.0 CD B:GLN255 4.6 36.1 1.0 CA B:LEU239 4.6 34.2 1.0 C3' D:U15 4.7 71.8 0.8 OE1 B:GLN255 4.7 38.5 1.0 O3' D:U15 4.7 74.6 0.8 N B:GLU240 4.8 31.6 1.0 C B:ASP238 4.8 33.0 1.0 O3' D:U14 4.8 79.9 0.8 CA B:ASP238 4.8 31.9 1.0 O D:HOH112 4.9 38.0 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