Magnesium in PDB 8a5f: Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant, PDB code: 8a5f was solved by P.T.Borges, F.Rollo, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.82 / 1.38
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	179.318, 38.04, 36.353, 90, 90.96, 90
R / Rfree (%)	15.1 / 18

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Magnesium atom in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant (pdb code 8a5f). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant, PDB code: 8a5f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant


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 Deinococcus Radiodurans Endonuclease III-1 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:40.7 occ:1.00 O A:GLY128 2.2 47.1 1.0 O A:ALA125 2.4 43.0 1.0 O A:HOH420 2.4 41.1 1.0 O A:ILE122 2.4 39.3 1.0 O A:GLY127 2.4 44.7 1.0 O A:LYS123 2.8 44.0 1.0 C A:GLY127 3.0 44.0 1.0 C A:GLY128 3.2 48.2 1.0 C A:LYS123 3.3 41.6 1.0 C A:ALA125 3.3 41.6 1.0 C A:ILE122 3.5 37.5 1.0 CA A:LYS123 3.5 40.3 1.0 N A:GLY128 3.6 44.6 1.0 CA A:GLY128 3.6 44.1 1.0 N A:ALA125 3.8 43.8 1.0 CA A:ALA125 3.9 40.9 1.0 CA A:GLY127 3.9 44.4 1.0 N A:LYS123 4.0 38.1 1.0 C A:PRO126 4.0 42.4 1.0 O A:PRO126 4.0 44.7 1.0 N A:GLY127 4.0 41.1 1.0 CB A:ALA125 4.1 41.2 1.0 N A:ALA124 4.3 42.1 1.0 N A:PRO126 4.4 44.5 1.0 C A:ALA124 4.4 42.8 1.0 N A:TYR129 4.4 45.1 1.0 O A:ASP130 4.6 46.7 1.0 CA A:PRO126 4.6 44.2 1.0 CG2 A:ILE122 4.7 35.9 1.0 CA A:ILE122 4.8 36.7 1.0 N A:ASP130 4.9 51.1 1.0 CA A:ALA124 4.9 39.8 1.0 CA A:TYR129 4.9 44.1 1.0 CB A:LYS123 4.9 40.2 1.0 OD1 A:ASP130 5.0 67.0 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 R61Q Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:34.8 occ:1.00 O A:THR147 2.3 34.6 1.0 O A:VAL152 2.4 31.1 1.0 O A:HOH494 2.4 44.5 1.0 O A:LEU149 2.4 35.1 1.0 O A:HOH531 2.6 49.2 1.0 C A:THR147 3.4 33.1 1.0 C A:VAL152 3.4 30.5 1.0 C A:LEU149 3.5 35.9 1.0 N A:VAL152 3.6 30.0 1.0 CA A:VAL152 4.0 27.4 1.0 N A:LEU149 4.0 32.5 1.0 CA A:THR147 4.1 28.6 1.0 N A:GLY151 4.1 33.6 1.0 C A:ASP148 4.1 35.4 1.0 N A:ASP148 4.3 31.8 1.0 CA A:PRO150 4.4 33.7 1.0 N A:PRO150 4.4 32.2 1.0 CA A:LEU149 4.4 34.2 1.0 CB A:VAL152 4.4 28.8 1.0 O A:ASP148 4.5 38.8 1.0 C A:PRO150 4.5 33.9 1.0 CA A:ASP148 4.5 34.4 1.0 N A:GLY153 4.5 27.8 1.0 C A:GLY151 4.6 34.6 1.0 O A:LEU146 4.6 28.6 1.0 O A:HOH541 4.7 44.7 1.0 CB A:THR147 4.8 31.4 1.0 CA A:GLY151 4.9 31.6 1.0 CA A:GLY153 4.9 31.0 1.0

F.Rollo, P.T.Borges, C.M.Silveira, M.T.G.Rosa, S.Todorovic, E.Moe. Disentangling Unusual Catalytic Properties and the Role of the [4FE-4S] Cluster of Three Endonuclease III From the Extremophile D. Radiodurans. Molecules V. 27 2022.
ISSN: ESSN 1420-3049
PubMed: 35807515
DOI: 10.3390/MOLECULES27134270