Magnesium in PDB 9byt: Class 1 Model For Turnover Condition of Bacillus Subtilis Ribonucleotide Reductase Complex

All present enzymatic activity of Class 1 Model For Turnover Condition of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;

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

Magnesium binding site 1 out of 2 in the Class 1 Model For Turnover 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 1 Model For Turnover Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg804 b:18.3 occ:1.00 O2A A:TTP803 2.1 31.5 1.0 O1G A:TTP803 2.4 32.1 1.0 O1B A:TTP803 2.8 27.8 1.0 PA A:TTP803 3.3 19.2 1.0 O3A A:TTP803 3.5 30.6 1.0 PB A:TTP803 3.7 31.6 1.0 PG A:TTP803 3.7 26.8 1.0 O A:ASP177 3.7 35.4 1.0 O5' A:TTP803 3.9 23.9 1.0 NH2 A:ARG207 4.0 19.3 1.0 CB A:SER178 4.1 16.6 1.0 O3B A:TTP803 4.2 28.0 1.0 O3G A:TTP803 4.2 18.4 1.0 O1A A:TTP803 4.5 19.6 1.0 CA A:SER178 4.5 17.4 1.0 C A:ASP177 4.8 24.9 1.0 O2G A:TTP803 4.8 34.9 1.0 C5' A:TTP803 5.0 21.4 1.0

Magnesium binding site 2 out of 2 in the Class 1 Model For Turnover 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 1 Model For Turnover Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:37.6 occ:1.00 O2A B:TTP801 2.0 22.2 1.0 O3G B:TTP801 2.2 34.5 1.0 O1B B:TTP801 2.5 32.1 1.0 PA B:TTP801 3.4 24.1 1.0 PG B:TTP801 3.4 31.3 1.0 PB B:TTP801 3.6 29.6 1.0 O1G B:TTP801 3.9 34.1 1.0 O B:ASP177 3.9 27.0 1.0 O3B B:TTP801 3.9 19.3 1.0 O3A B:TTP801 4.0 32.5 1.0 CB B:SER178 4.1 14.3 1.0 NH2 B:ARG207 4.1 20.8 1.0 O1A B:TTP801 4.2 30.2 1.0 C5' B:TTP801 4.4 24.4 1.0 O5' B:TTP801 4.5 24.9 1.0 CA B:SER178 4.6 18.4 1.0 O2G B:TTP801 4.6 23.3 1.0 O2B B:TTP801 4.9 29.3 1.0 C B:ASP177 5.0 23.7 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