Manganese in PDB 9by3: Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex

All present enzymatic activity of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;

The structure of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Manganese atom in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex (pdb code 9by3). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9by3:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn401 b:25.1 occ:0.85 OE2 C:GLU97 2.0 29.2 1.0 OE2 C:GLU164 2.0 28.6 1.0 OE1 C:GLU164 2.1 28.8 1.0 OE1 C:GLU198 2.2 27.6 1.0 CD C:GLU164 2.3 29.2 1.0 ND1 C:HIS201 2.4 20.7 1.0 CD C:GLU97 2.8 26.3 1.0 OE1 C:GLU97 3.0 29.9 1.0 CG C:HIS201 3.3 21.8 1.0 CD C:GLU198 3.4 26.3 1.0 CE1 C:HIS201 3.4 22.3 1.0 CB C:HIS201 3.5 21.8 1.0 MN C:MN402 3.7 26.4 0.8 CG C:GLU164 3.9 27.1 1.0 OE2 C:GLU198 4.1 26.9 1.0 CA C:GLU198 4.2 24.2 1.0 CG C:GLU97 4.2 24.4 1.0 CB C:GLU198 4.4 24.1 1.0 CG C:GLN69 4.4 24.3 1.0 CG C:GLU198 4.4 25.0 1.0 NE2 C:HIS201 4.5 22.5 1.0 CD2 C:HIS201 4.5 22.1 1.0 CE2 C:PHE168 4.6 30.2 1.0 NE2 C:GLN69 4.8 27.7 1.0 CB C:GLU164 4.8 26.2 1.0 OD1 C:ASP66 4.9 27.5 1.0 CE1 C:HIS101 5.0 22.6 1.0 N C:GLU198 5.0 23.9 1.0

Manganese binding site 2 out of 4 in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Mn402 b:26.4 occ:0.85 OD1 C:ASP66 2.0 27.5 1.0 OE2 C:GLU198 2.1 26.9 1.0 OE1 C:GLU97 2.1 29.9 1.0 ND1 C:HIS101 2.2 22.8 1.0 OE1 C:GLU198 2.7 27.6 1.0 CD C:GLU198 2.7 26.3 1.0 CG C:ASP66 2.9 24.6 1.0 CE1 C:HIS101 3.1 22.6 1.0 OD2 C:ASP66 3.1 28.0 1.0 CD C:GLU97 3.2 26.3 1.0 CG C:HIS101 3.2 23.0 1.0 CB C:HIS101 3.6 23.3 1.0 OE2 C:GLU97 3.7 29.2 1.0 MN C:MN401 3.7 25.1 0.8 CZ C:PHE168 3.9 29.8 1.0 CA C:GLU97 4.2 22.0 1.0 CG C:GLU198 4.2 25.0 1.0 CE2 C:PHE168 4.2 30.2 1.0 NE2 C:HIS101 4.2 21.8 1.0 CB C:ASP66 4.3 22.2 1.0 CD2 C:HIS101 4.3 23.2 1.0 CG2 C:ILE194 4.4 21.9 1.0 CG C:GLU97 4.4 24.4 1.0 CB C:GLU97 4.5 22.0 1.0 CE1 C:PHE168 4.8 28.5 1.0 O C:GLU97 4.8 22.2 1.0 N C:GLU97 4.9 21.2 1.0 CA C:ASP66 4.9 22.0 1.0 OE1 C:GLU164 4.9 28.8 1.0

Manganese binding site 3 out of 4 in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn401 b:22.5 occ:1.00 OE2 D:GLU97 1.9 27.5 1.0 OE1 D:GLU198 2.1 25.1 1.0 OE1 D:GLU164 2.3 28.0 1.0 OE2 D:GLU164 2.3 25.5 1.0 ND1 D:HIS201 2.3 18.4 1.0 CD D:GLU164 2.7 24.2 1.0 CD D:GLU97 2.9 24.1 1.0 CD D:GLU198 3.1 24.0 1.0 OE1 D:GLU97 3.2 26.4 1.0 CE1 D:HIS201 3.2 18.3 1.0 CG D:HIS201 3.4 19.2 1.0 OE2 D:GLU198 3.7 24.5 1.0 CB D:HIS201 3.7 19.8 1.0 MN D:MN402 3.9 24.7 1.0 CA D:GLU198 4.2 20.7 1.0 CG D:GLU164 4.2 22.2 1.0 CG D:GLU97 4.3 23.1 1.0 CG D:GLN69 4.3 27.8 1.0 CG D:GLU198 4.3 22.0 1.0 NE2 D:HIS201 4.4 20.0 1.0 CB D:GLU198 4.4 20.6 1.0 CE D:MET74 4.5 28.9 1.0 OD1 D:ASP66 4.5 26.9 1.0 CD2 D:HIS201 4.5 17.6 1.0 N D:GLU198 4.8 20.6 1.0 CE2 D:PHE168 4.8 22.1 1.0 CE1 D:HIS101 4.9 19.9 1.0 NE2 D:GLN69 4.9 28.2 1.0 ND1 D:HIS101 5.0 20.5 1.0

Manganese binding site 4 out of 4 in the Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Class 3 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Mn402 b:24.7 occ:1.00 OE1 D:GLU97 2.0 26.4 1.0 OE2 D:GLU198 2.1 24.5 1.0 ND1 D:HIS101 2.1 20.5 1.0 OD2 D:ASP66 2.2 23.1 1.0 OD1 D:ASP66 2.3 26.9 1.0 CG D:ASP66 2.5 25.8 1.0 CD D:GLU198 3.0 24.0 1.0 CE1 D:HIS101 3.1 19.9 1.0 CG D:HIS101 3.2 22.8 1.0 CD D:GLU97 3.2 24.1 1.0 OE1 D:GLU198 3.2 25.1 1.0 CB D:HIS101 3.5 23.2 1.0 OE2 D:GLU97 3.8 27.5 1.0 MN D:MN401 3.9 22.5 1.0 CB D:ASP66 4.0 25.5 1.0 CA D:GLU97 4.2 23.5 1.0 NE2 D:HIS101 4.2 21.6 1.0 CD2 D:HIS101 4.3 21.0 1.0 CG D:GLU97 4.3 23.1 1.0 CB D:GLU97 4.3 23.1 1.0 CG D:GLU198 4.4 22.0 1.0 CG2 D:ILE194 4.5 20.2 1.0 CA D:ASP66 4.9 25.8 1.0 N D:GLU97 4.9 22.7 1.0 CZ D:PHE168 5.0 22.6 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