Magnesium in PDB 4unf: Crystal Structure of Deinococcus Radiodurans Endonuclease III-1

All present enzymatic activity of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1:
4.2.99.18;

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1, PDB code: 4unf was solved by A.Sarre, M.Okvist, T.Klar, D.Hall, A.O.Smalas, S.Mcsweeney, J.Timmins, E.Moe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.192 / 2.15
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	181.380, 38.558, 37.094, 90.00, 89.34, 90.00
R / Rfree (%)	15.31 / 19.43

The structure of Crystal Structure of Deinococcus Radiodurans Endonuclease III-1 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 (pdb code 4unf). 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, PDB code: 4unf:
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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1249 b:60.5 occ:1.00 O A:ALA118 2.3 61.7 1.0 O A:GLY121 2.3 66.1 1.0 O A:ILE115 2.4 59.5 1.0 O A:HOH2067 2.5 86.5 1.0 O A:GLY120 2.6 59.4 1.0 O A:LYS116 2.7 60.5 1.0 C A:LYS116 3.1 59.2 1.0 C A:ALA118 3.1 63.2 1.0 C A:GLY120 3.2 62.7 1.0 CA A:LYS116 3.4 55.2 1.0 C A:GLY121 3.4 69.2 1.0 C A:ILE115 3.5 53.5 1.0 N A:ALA118 3.5 62.2 1.0 O A:HOH2068 3.5 55.5 1.0 CA A:ALA118 3.7 62.7 1.0 N A:GLY121 3.7 62.4 1.0 CA A:GLY121 3.8 68.2 1.0 N A:LYS116 3.9 54.3 1.0 C A:PRO119 4.0 65.8 1.0 CB A:ALA118 4.0 52.3 1.0 O A:PRO119 4.0 63.6 1.0 N A:GLY120 4.1 59.5 1.0 CA A:GLY120 4.1 59.8 1.0 N A:ALA117 4.1 60.8 1.0 N A:PRO119 4.2 67.1 1.0 C A:ALA117 4.3 63.7 1.0 CA A:PRO119 4.5 71.3 1.0 O A:ASP123 4.6 57.3 1.0 N A:TYR122 4.6 65.9 1.0 N A:ASP123 4.7 57.4 1.0 CB A:LYS116 4.8 51.8 1.0 CA A:ALA117 4.8 64.6 1.0 CG2 A:ILE115 4.8 47.0 1.0 CA A:ILE115 4.8 48.7 1.0 O A:ALA117 5.0 57.0 1.0

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


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1250 b:60.6 occ:1.00 O A:THR140 2.0 50.7 1.0 O A:HOH2077 2.6 63.8 1.0 O A:VAL145 2.6 47.8 1.0 O A:LEU142 2.7 53.3 1.0 O A:HOH2074 3.0 63.4 1.0 C A:THR140 3.2 47.5 1.0 C A:VAL145 3.7 49.9 1.0 C A:LEU142 3.7 54.8 1.0 N A:VAL145 3.9 49.3 1.0 CA A:THR140 4.0 43.9 1.0 C A:ASP141 4.1 51.8 1.0 N A:LEU142 4.1 45.7 1.0 N A:ASP141 4.2 45.2 1.0 CA A:VAL145 4.2 46.4 1.0 O A:ASP141 4.3 54.5 1.0 CA A:ASP141 4.4 52.3 1.0 N A:GLY144 4.4 52.0 1.0 CA A:LEU142 4.6 45.7 1.0 N A:PRO143 4.6 59.6 1.0 CB A:VAL145 4.6 47.2 1.0 CA A:PRO143 4.6 54.6 1.0 CB A:THR140 4.7 46.1 1.0 O A:HOH2043 4.7 56.2 1.0 C A:PRO143 4.8 55.1 1.0 N A:GLY146 4.8 48.5 1.0 O A:LEU139 4.8 41.7 1.0 C A:GLY144 4.9 54.5 1.0

A.Sarre, M.Okvist, T.Klar, D.R.Hall, A.O.Smalas, S.Mcsweeney, J.Timmins, E.Moe. Structural and Functional Characterization of Two Unusual Endonuclease III Enzymes From Deinococcus Radiodurans. J.Struct.Biol. V. 191 87 2015.
ISSN: ISSN 1047-8477
PubMed: 26172070
DOI: 10.1016/J.JSB.2015.05.009