Magnesium in PDB 4rd1: Structure of AIF2 Gamma Mutant From S. Solfataricus

The structure of Structure of AIF2 Gamma Mutant From S. Solfataricus, PDB code: 4rd1 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)	44.11 / 1.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.320, 60.610, 144.600, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 18.9

The binding sites of Magnesium atom in the Structure of AIF2 Gamma Mutant From S. Solfataricus (pdb code 4rd1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of AIF2 Gamma Mutant From S. Solfataricus, PDB code: 4rd1:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of AIF2 Gamma Mutant From S. Solfataricus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of AIF2 Gamma Mutant From S. Solfataricus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg503 b:20.7 occ:1.00 O2G A:GTP501 1.9 35.5 0.8 O A:HOH606 2.0 20.7 1.0 OG1 A:THR46 2.1 21.4 1.0 O3B A:GDP502 2.1 20.6 0.2 OG1 A:THR23 2.1 23.1 1.0 O A:HOH611 2.1 23.4 1.0 O2B A:GTP501 2.2 24.6 0.8 O3 A:PO4505 2.3 22.3 0.2 CB A:THR46 3.0 21.7 1.0 PG A:GTP501 3.1 32.9 0.8 CB A:THR23 3.2 22.1 1.0 PB A:GTP501 3.4 24.3 0.8 PB A:GDP502 3.4 23.0 0.2 O3B A:GTP501 3.5 29.0 0.8 O2B A:GDP502 3.7 20.5 0.2 P A:PO4505 3.8 20.6 0.2 N A:THR46 3.9 24.1 1.0 N A:THR23 3.9 21.5 1.0 O3G A:GTP501 4.0 36.1 0.8 CA A:THR46 4.0 24.3 1.0 CG2 A:THR46 4.1 20.6 1.0 CA A:THR23 4.1 23.2 1.0 OD2 A:ASP93 4.1 23.0 1.0 OD1 A:ASP93 4.2 22.4 1.0 O1G A:GTP501 4.3 32.9 0.8 O1B A:GDP502 4.3 23.9 0.2 O2A A:GDP502 4.3 23.6 0.2 CG2 A:THR23 4.3 23.4 1.0 O1B A:GTP501 4.3 22.7 0.8 O A:HOH674 4.4 28.6 1.0 O2A A:GTP501 4.4 25.7 0.8 O2 A:PO4505 4.5 19.1 0.2 O A:HOH628 4.5 23.0 1.0 CE A:LYS22 4.5 19.8 1.0 O3A A:GTP501 4.5 23.1 0.8 O3A A:GDP502 4.5 24.2 0.2 CG A:ASP93 4.6 22.4 1.0 O A:ALA94 4.6 20.6 1.0 CB A:LYS22 4.6 21.1 1.0 O1 A:PO4505 4.6 14.7 0.2 O A:HOH648 4.6 33.1 1.0 O4 A:PO4505 4.6 19.0 0.2 PA A:GTP501 4.7 25.7 0.8 PA A:GDP502 4.7 25.1 0.2 O1A A:GDP502 4.8 23.8 0.2 O1A A:GTP501 4.8 25.8 0.8 C A:LYS22 4.9 19.8 1.0 C A:MET45 4.9 28.3 1.0 NZ A:LYS22 5.0 19.7 1.0

Magnesium binding site 2 out of 2 in the Structure of AIF2 Gamma Mutant From S. Solfataricus


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of AIF2 Gamma Mutant From S. Solfataricus within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:43.8 occ:0.83 O A:HOH648 2.0 33.1 1.0 O A:GLY44 2.1 43.0 1.0 O A:HOH888 2.1 40.1 1.0 OD1 A:ASP19 2.1 38.5 1.0 O A:HOH887 2.3 66.4 1.0 O A:HOH699 2.4 36.0 1.0 CG A:ASP19 3.1 35.8 1.0 C A:GLY44 3.3 36.2 1.0 OD2 A:ASP19 3.5 40.2 1.0 O2 A:PO4505 3.9 19.1 0.2 CA A:MET45 3.9 32.4 0.5 CA A:MET45 3.9 30.6 0.5 O3G A:GTP501 4.0 36.1 0.8 O2A A:GDP502 4.0 23.6 0.2 N A:MET45 4.0 32.6 1.0 CB A:MET45 4.1 36.9 0.5 O A:HOH679 4.1 31.1 1.0 O2B A:GDP502 4.2 20.5 0.2 CB A:MET45 4.2 31.3 0.5 O2A A:GTP501 4.3 25.7 0.8 O3B A:GTP501 4.3 29.0 0.8 CA A:GLY44 4.4 37.9 1.0 C5' A:GDP502 4.4 29.5 0.2 CB A:ASP19 4.5 31.9 1.0 O A:ARG43 4.6 38.8 1.0 C5' A:GTP501 4.7 28.3 0.8 CA A:ASP19 4.8 27.8 1.0 PG A:GTP501 4.9 32.9 0.8

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