Magnesium in PDB 5nkk: SMG8-SMG9 Complex Gdp Bound

The structure of SMG8-SMG9 Complex Gdp Bound, PDB code: 5nkk was solved by L.Li, J.Basquin, E.Conti, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.89 / 2.64
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	110.605, 110.605, 360.266, 90.00, 90.00, 120.00
R / Rfree (%)	23.2 / 27.4

The binding sites of Magnesium atom in the SMG8-SMG9 Complex Gdp Bound (pdb code 5nkk). 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 SMG8-SMG9 Complex Gdp Bound, PDB code: 5nkk:

Magnesium binding site 1 out of 1 in the SMG8-SMG9 Complex Gdp Bound


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of SMG8-SMG9 Complex Gdp Bound within 5.0Å range: probe atom residue distance (Å) B Occ F:Mg402 b:0.5 occ:1.00 OG F:SER100 2.1 0.0 1.0 O3B F:GDP401 2.2 0.4 1.0 O F:HOH502 2.5 71.5 1.0 CB F:SER100 3.0 0.7 1.0 O1B F:GDP401 3.2 0.3 1.0 PB F:GDP401 3.2 0.3 1.0 O1A F:GDP401 3.6 0.3 1.0 OD1 F:ASP150 3.9 84.6 1.0 O3A F:GDP401 4.2 0.4 1.0 O F:ARG121 4.2 0.8 1.0 CA F:SER100 4.3 0.7 1.0 PA F:GDP401 4.3 0.7 1.0 O2B F:GDP401 4.3 0.0 1.0 N F:SER100 4.4 0.1 1.0 O2A F:GDP401 4.6 95.0 1.0 OD2 F:ASP150 4.6 84.6 1.0 N F:VAL123 4.6 0.7 1.0 CB F:VAL123 4.7 0.0 1.0 CG F:ASP150 4.7 83.8 1.0

L.Li, M.Lingaraju, C.Basquin, J.Basquin, E.Conti. Structure of A SMG8-SMG9 Complex Identifies A G-Domain Heterodimer in the Nmd Effector Proteins. Rna V. 23 1028 2017.
ISSN: ESSN 1469-9001
PubMed: 28389433
DOI: 10.1261/RNA.061200.117