Magnesium in PDB 4rd3: Structure of AIF2GAMMA Variant in the Presence of Nucleotide

The structure of Structure of AIF2GAMMA Variant in the Presence of Nucleotide, PDB code: 4rd3 was solved by E.Dubiez, A.Aleksandrov, C.Lazennec-Schurdevin, Y.Mechulam, E.Schmitt, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.36 / 1.69
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.320, 60.460, 144.470, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 22.3

The binding sites of Magnesium atom in the Structure of AIF2GAMMA Variant in the Presence of Nucleotide (pdb code 4rd3). 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 AIF2GAMMA Variant in the Presence of Nucleotide, PDB code: 4rd3:

Magnesium binding site 1 out of 1 in the Structure of AIF2GAMMA Variant in the Presence of Nucleotide


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of AIF2GAMMA Variant in the Presence of Nucleotide within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:25.2 occ:1.00 OG1 A:THR23 2.1 22.7 1.0 O3 A:PO4501 2.1 30.1 1.0 O A:HOH603 2.1 22.2 1.0 O3B A:GDP502 2.2 26.7 1.0 OG1 A:THR46 2.2 22.5 1.0 O A:HOH631 2.2 22.1 1.0 CB A:THR46 3.1 24.4 1.0 CB A:THR23 3.2 23.6 1.0 PB A:GDP502 3.4 26.4 1.0 P A:PO4501 3.6 32.7 1.0 O1B A:GDP502 3.7 26.9 1.0 N A:THR46 3.7 26.3 1.0 N A:THR23 3.9 18.9 1.0 CA A:THR46 4.0 26.8 1.0 OD2 A:ASP93 4.1 25.9 1.0 CA A:THR23 4.1 24.1 1.0 O2 A:PO4501 4.2 35.6 1.0 CG2 A:THR46 4.2 19.3 1.0 O A:HOH681 4.3 26.9 1.0 O1 A:PO4501 4.3 25.9 1.0 CG2 A:THR23 4.3 24.6 1.0 OD1 A:ASP93 4.3 25.2 1.0 O2B A:GDP502 4.3 21.9 1.0 O2A A:GDP502 4.4 27.1 1.0 CE A:LYS22 4.5 22.7 1.0 O A:HOH645 4.5 26.8 1.0 O4 A:PO4501 4.5 31.0 1.0 CB A:LYS22 4.5 22.5 1.0 O A:ALA94 4.6 23.1 1.0 O3A A:GDP502 4.6 25.2 1.0 CG A:ASP93 4.6 24.7 1.0 C A:MET45 4.8 29.7 1.0 PA A:GDP502 4.8 26.6 1.0 O1A A:GDP502 4.8 28.4 1.0 NZ A:LYS22 4.9 22.1 1.0 O A:HOH611 4.9 30.6 1.0 C A:LYS22 4.9 21.7 1.0

E.Dubiez, A.Aleksandrov, C.Lazennec-Schurdevin, Y.Mechulam, E.Schmitt. Identification of A Second Gtp-Bound Magnesium Ion in Archaeal Initiation Factor 2. Nucleic Acids Res. V. 43 2946 2015.
ISSN: ISSN 0305-1048
PubMed: 25690901
DOI: 10.1093/NAR/GKV053