Magnesium in PDB 8a5c: Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L Variant, PDB code: 8a5c 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)	44.63 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	178.526, 37.827, 36.55, 90, 90.61, 90
R / Rfree (%)	19.4 / 24.7

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L 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 Y100L Variant (pdb code 8a5c). 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 Y100L Variant, PDB code: 8a5c:
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 Y100L 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 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:79.2 occ:1.00 O A:GLY127 2.0 141.9 1.0 O A:ALA125 2.4 93.9 1.0 O A:GLY128 2.5 123.6 1.0 O A:ILE122 2.8 83.8 1.0 C A:GLY127 2.9 130.6 1.0 C A:ALA125 3.2 91.0 1.0 O A:LYS123 3.4 81.4 1.0 C A:GLY128 3.4 128.5 1.0 CA A:GLY127 3.7 120.3 1.0 N A:GLY127 3.7 105.9 1.0 N A:GLY128 3.8 133.0 1.0 C A:PRO126 3.8 98.9 1.0 C A:LYS123 3.9 77.0 1.0 CA A:ALA125 3.9 85.0 1.0 N A:ALA125 3.9 87.2 1.0 O A:ASP130 3.9 106.8 1.0 C A:ILE122 3.9 71.4 1.0 CA A:GLY128 3.9 134.2 1.0 O A:PRO126 4.0 104.2 1.0 CB A:ALA125 4.0 82.0 1.0 CA A:LYS123 4.0 80.5 1.0 N A:PRO126 4.1 102.4 1.0 N A:TYR129 4.4 121.6 1.0 N A:ASP130 4.4 96.0 1.0 CA A:PRO126 4.4 94.1 1.0 N A:LYS123 4.5 75.1 1.0 C A:ALA124 4.7 80.3 1.0 CA A:TYR129 4.8 99.5 1.0 CG2 A:ILE122 4.8 76.1 1.0 N A:ALA124 4.8 81.1 1.0 C A:ASP130 5.0 102.7 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 Y100L 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 Y100L Variant within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:91.8 occ:1.00 O A:VAL152 2.6 68.6 1.0 O A:THR147 3.0 80.5 1.0 O A:LEU149 3.1 77.5 1.0 C A:VAL152 3.6 71.5 1.0 N A:VAL152 3.8 64.0 1.0 C A:THR147 4.0 73.3 1.0 C A:LEU149 4.1 75.0 1.0 N A:GLY151 4.1 70.8 1.0 CA A:VAL152 4.3 66.1 1.0 N A:GLY153 4.5 62.7 1.0 CA A:PRO150 4.5 71.6 1.0 C A:GLY151 4.6 68.4 1.0 CA A:THR147 4.6 63.2 1.0 C A:PRO150 4.6 73.1 1.0 N A:LEU149 4.7 74.6 1.0 CA A:GLY153 4.7 65.8 1.0 N A:PRO150 4.8 69.3 1.0 CA A:GLY151 4.8 74.1 1.0 CB A:VAL152 4.9 64.1 1.0 C A:ASP148 4.9 80.3 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