Magnesium in PDB 9bzd: Class 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex

All present enzymatic activity of Class 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;

The structure of Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex (pdb code 9bzd). 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 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9bzd:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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