Magnesium in PDB 9by0: Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex

All present enzymatic activity of Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;

The structure of Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Magnesium atom in the Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex (pdb code 9by0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9by0:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:39.7 occ:1.00 O2A A:TTP801 2.1 43.3 1.0 O1B A:TTP801 2.9 47.0 1.0 O2G A:TTP801 3.4 48.6 1.0 PA A:TTP801 3.6 38.7 1.0 CB A:SER178 3.6 36.7 1.0 O A:ASP177 3.8 46.1 1.0 PB A:TTP801 4.0 46.2 1.0 O1A A:TTP801 4.2 42.7 1.0 CA A:SER178 4.2 33.5 1.0 PG A:TTP801 4.3 47.9 1.0 O3A A:TTP801 4.3 48.3 1.0 O3B A:TTP801 4.4 43.0 1.0 O1G A:TTP801 4.5 48.8 1.0 C5' A:TTP801 4.6 41.8 1.0 O5' A:TTP801 4.6 31.3 1.0 NH1 A:ARG207 4.7 42.7 1.0 C A:ASP177 4.8 39.4 1.0 OG A:SER178 4.8 41.9 1.0 N A:SER178 5.0 33.0 1.0

Magnesium binding site 2 out of 2 in the Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Class 16 Model For Pre-Reduction Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:23.0 occ:1.00 O2A B:TTP802 2.2 36.0 1.0 O3G B:TTP802 2.5 41.4 1.0 O1B B:TTP802 2.9 39.3 1.0 PA B:TTP802 3.6 38.1 1.0 O B:ASP177 3.7 36.8 1.0 PG B:TTP802 3.8 34.0 1.0 CB B:SER178 3.9 20.2 1.0 PB B:TTP802 3.9 40.7 1.0 O1G B:TTP802 4.1 30.2 1.0 O3A B:TTP802 4.1 38.5 1.0 O3B B:TTP802 4.4 37.8 1.0 CA B:SER178 4.5 26.5 1.0 O1A B:TTP802 4.5 32.8 1.0 NH1 B:ARG207 4.5 35.6 1.0 C5' B:TTP802 4.6 31.8 1.0 O5' B:TTP802 4.6 30.7 1.0 C B:ASP177 4.8 35.9 1.0 O2G B:TTP802 5.0 39.8 1.0

D.Xu, W.C.Thomas, A.A.Burnim, N.Ando. Conformational Landscapes of A Class I Ribonucleotide Reductase Complex During Turnover Reveal Intrinsic Dynamics and Asymmetry Nat Commun V. 16 2458 2025.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-025-57735-4