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Manganese in PDB 6tqz: Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions, PDB code: 6tqz was solved by K.Grave, M.Hogbom, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.02 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.019, 60.124, 96.048, 90.00, 106.59, 90.00
R / Rfree (%) 16.6 / 22.2

Other elements in 6tqz:

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions (pdb code 6tqz). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 2 binding sites of Manganese where determined in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions, PDB code: 6tqz:
Jump to Manganese binding site number: 1; 2;

Manganese binding site 1 out of 2 in 6tqz

Go back to Manganese Binding Sites List in 6tqz
Manganese binding site 1 out of 2 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn406

b:47.3
occ:0.58
 OE1 A:GLU195 1.8 47.0 1.0
OE2 A:GLU93 1.9 40.8 1.0
OD1 A:ASP62 2.2 36.6 1.0
CD A:GLU195 2.5 43.8 1.0
OE2 A:GLU195 2.7 44.6 1.0
CD A:GLU93 2.7 31.3 1.0
FE A:FE2401 2.8 40.8 0.7
OE1 A:GLU93 2.9 33.9 1.0
OE2 A:GLU161 3.3 42.9 1.0
CG A:ASP62 3.3 30.6 1.0
HE2 A:PHE165 3.4 67.9 1.0
ND1 A:HIS96 3.5 23.4 1.0
CE2 A:PHE165 3.8 56.6 1.0
HZ A:PHE165 3.8 61.0 1.0
HA A:ASP62 3.8 32.0 1.0
HA A:GLU93 3.9 27.3 1.0
CG A:GLU195 3.9 36.1 1.0
HE1 A:HIS96 3.9 25.8 1.0
OD2 A:ASP62 4.0 38.2 1.0
CZ A:PHE165 4.1 50.8 1.0
CE1 A:HIS96 4.1 21.5 1.0
CG A:GLU93 4.1 25.3 1.0
HG3 A:GLU195 4.1 43.3 1.0
HG3 A:GLN65 4.1 40.6 1.0
HG2 A:GLU195 4.2 43.3 1.0
HB3 A:GLU93 4.2 25.4 1.0
CD A:GLU161 4.3 43.7 1.0
HB2 A:GLN65 4.4 35.3 1.0
CB A:ASP62 4.4 29.8 1.0
CB A:GLU93 4.5 21.1 1.0
HG3 A:GLU93 4.5 30.3 1.0
CA A:ASP62 4.6 26.7 1.0
HB2 A:HIS96 4.6 26.6 1.0
HB3 A:ASP62 4.6 35.7 1.0
CA A:GLU93 4.6 22.8 1.0
HG2 A:GLU93 4.7 30.3 1.0
HB3 A:GLN65 4.7 35.3 1.0
ND1 A:HIS198 4.7 24.6 1.0
CG A:HIS96 4.7 21.4 1.0
OE1 A:GLU161 4.7 49.3 1.0
CD2 A:PHE165 4.7 58.7 1.0
HG23 A:ILE191 4.8 24.4 1.0
HA A:GLU195 4.8 29.3 1.0
HE1 A:HIS198 4.8 29.1 1.0
CB A:GLN65 4.9 29.4 1.0
CG A:GLN65 4.9 33.8 1.0
HD2 A:PHE165 4.9 70.5 1.0
HD21 A:LEU160 5.0 47.0 1.0
CB A:GLU195 5.0 30.7 1.0
HB3 A:GLU195 5.0 36.9 1.0
HA A:GLU161 5.0 39.0 1.0

Manganese binding site 2 out of 2 in 6tqz

Go back to Manganese Binding Sites List in 6tqz
Manganese binding site 2 out of 2 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Aerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn404

b:41.8
occ:0.54
 OE1 B:GLU195 1.7 40.0 1.0
OE2 B:GLU93 1.9 46.7 1.0
OD1 B:ASP62 1.9 33.7 1.0
CD B:GLU195 2.5 40.3 1.0
CD B:GLU93 2.8 28.2 1.0
ND1 B:HIS96 2.9 30.0 1.0
OE2 B:GLU195 2.9 52.2 1.0
HE2 B:PHE165 3.0 57.5 1.0
OE1 B:GLU93 3.0 39.3 1.0
CG B:ASP62 3.1 30.8 1.0
FE B:FE2401 3.1 49.8 0.8
HE1 B:HIS96 3.5 30.0 1.0
CE1 B:HIS96 3.6 30.0 1.0
HA B:GLU93 3.6 24.3 1.0
OD2 B:ASP62 3.6 37.8 1.0
OE1 B:GLU161 3.8 49.8 1.0
CG B:GLU195 3.8 33.0 1.0
CE2 B:PHE165 3.9 47.9 1.0
HG2 B:GLU195 4.0 39.5 1.0
CG B:HIS96 4.0 30.0 1.0
HA B:ASP62 4.1 31.4 1.0
HG3 B:GLU195 4.1 39.5 1.0
HB2 B:HIS96 4.1 30.0 1.0
CG B:GLU93 4.2 28.7 1.0
HG23 B:ILE191 4.2 24.0 1.0
CB B:ASP62 4.3 18.4 1.0
HB3 B:GLU93 4.3 24.9 1.0
HB3 B:HIS96 4.4 30.0 1.0
CB B:HIS96 4.4 30.0 1.0
CA B:GLU93 4.4 20.3 1.0
HB3 B:ASP62 4.5 22.1 1.0
HZ B:PHE165 4.5 56.9 1.0
CB B:GLU93 4.5 20.8 1.0
HD2 B:PHE165 4.6 63.2 1.0
HE1 B:HIS198 4.6 25.8 1.0
HG3 B:GLU93 4.7 34.5 1.0
CZ B:PHE165 4.7 47.4 1.0
CA B:ASP62 4.7 26.2 1.0
HG2 B:GLU93 4.7 34.5 1.0
ND1 B:HIS198 4.7 24.5 1.0
CD2 B:PHE165 4.7 52.7 1.0
HB2 B:GLN65 4.8 29.9 1.0
CD B:GLU161 4.8 55.9 1.0
NE2 B:HIS96 4.8 30.0 1.0
HG3 B:GLN65 4.9 39.3 1.0
HA B:GLU195 4.9 29.8 1.0
HG22 B:ILE191 4.9 24.0 1.0
CG2 B:ILE191 4.9 20.0 1.0

Reference:

K.Grave, J.J.Griese, G.Berggren, M.Bennett, M.Hogbom. The Bacillus Anthracis Class Ib Ribonucleotide Reductase Subunit Nrdf Intrinsically Selects Manganese Over Iron J.Biol.Inorg.Chem. 2020.
ISSN: ESSN 1432-1327
DOI: 10.1007/S00775-020-01782-3
Page generated: Sun Oct 6 07:12:24 2024

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