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

Enzymatic activity of 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;

Other elements in 9bzd:

The structure of Class 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 4 binding sites of Manganese where determined in the Class 23 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9bzd:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 9bzd

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Manganese binding site 1 out of 4 in the Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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 9bzd

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Manganese binding site 2 out of 4 in the Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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 9bzd

Go back to Manganese Binding Sites List in 9bzd
Manganese binding site 3 out of 4 in the Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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 9bzd

Go back to Manganese Binding Sites List in 9bzd
Manganese binding site 4 out of 4 in the Class 23 Model For Combined Refinement 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 23 Model For Combined Refinement 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

Reference:

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
Page generated: Sun Aug 17 02:19:14 2025

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