Manganese in PDB 9bzk: Class 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex
Enzymatic activity of Class 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex
All present enzymatic activity of Class 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex:
1.17.4.1;
Other elements in 9bzk:
The structure of Class 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Class 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex
(pdb code 9bzk). 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 43 Model For Combined Refinement of Bacillus Subtilis Ribonucleotide Reductase Complex, PDB code: 9bzk:
Jump to Manganese binding site number:
1;
2;
3;
4;
Manganese binding site 1 out
of 4 in 9bzk
Go back to
Manganese Binding Sites List in 9bzk
Manganese binding site 1 out
of 4 in the Class 43 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 43 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 9bzk
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Manganese Binding Sites List in 9bzk
Manganese binding site 2 out
of 4 in the Class 43 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 43 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 9bzk
Go back to
Manganese Binding Sites List in 9bzk
Manganese binding site 3 out
of 4 in the Class 43 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 43 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
|
CE2
|
D:PHE168
|
4.8
|
22.1
|
1.0
|
N
|
D:GLU198
|
4.8
|
20.6
|
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 9bzk
Go back to
Manganese Binding Sites List in 9bzk
Manganese binding site 4 out
of 4 in the Class 43 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 43 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 02:20:22 2025
|