Manganese in PDB 9byd: Class 16 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex

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

The structure of Class 16 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 16 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex (pdb code 9byd). 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 16 Model For Product Condition of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9byd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Class 16 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 16 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 16 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 16 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 16 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 16 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 16 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 16 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