Magnesium in PDB 9by8: Class 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex

All present enzymatic activity of Class 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;

The structure of Class 9 Model For Product 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 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex (pdb code 9by8). 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 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9by8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Class 9 Model For Product 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 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:24.1 occ:1.00 O2A A:TTP801 2.0 26.6 1.0 O2B A:TTP801 2.5 25.4 1.0 O1G A:TTP801 2.5 33.5 1.0 PA A:TTP801 3.5 19.4 1.0 PB A:TTP801 3.6 29.8 1.0 PG A:TTP801 3.8 32.2 1.0 O A:ASP177 3.9 27.4 1.0 O3A A:TTP801 4.0 35.0 1.0 CB A:SER178 4.0 19.3 1.0 O3B A:TTP801 4.1 28.4 1.0 O1A A:TTP801 4.2 21.9 1.0 O3G A:TTP801 4.5 34.8 1.0 C5' A:TTP801 4.5 25.0 1.0 CA A:SER178 4.5 18.1 1.0 O5' A:TTP801 4.5 18.8 1.0 NH2 A:ARG207 4.5 20.7 1.0 O2G A:TTP801 4.9 23.5 1.0 O1B A:TTP801 4.9 34.0 1.0 C A:ASP177 5.0 22.9 1.0

Magnesium binding site 2 out of 2 in the Class 9 Model For Product 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 9 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:27.3 occ:1.00 O3G B:TTP801 2.1 27.1 1.0 O2A B:TTP801 2.3 27.1 1.0 O2B B:TTP801 3.0 28.1 1.0 PA B:TTP801 3.4 22.9 1.0 PG B:TTP801 3.6 30.1 1.0 O3A B:TTP801 3.7 36.8 1.0 O B:ASP177 3.7 31.4 1.0 PB B:TTP801 3.8 32.4 1.0 O5' B:TTP801 4.0 24.1 1.0 NH2 B:ARG207 4.0 18.4 1.0 O3B B:TTP801 4.2 37.2 1.0 CB B:SER178 4.2 14.7 1.0 O1G B:TTP801 4.3 20.4 1.0 O2G B:TTP801 4.5 33.8 1.0 CA B:SER178 4.6 17.2 1.0 O1A B:TTP801 4.7 21.9 1.0 C B:ASP177 4.8 24.8 1.0 C5' B:TTP801 5.0 22.1 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