Iron 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:

Manganese (Mn) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron 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 Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6tqz

Go back to Iron Binding Sites List in 6tqz
Iron 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 Iron with other atoms in the Fe 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:Fe401

b:40.8
occ:0.72
 OE1 A:GLU93 1.8 33.9 1.0
OE2 A:GLU195 2.0 44.6 1.0
OE1 A:GLU161 2.3 49.3 1.0
OE2 A:GLU161 2.3 42.9 1.0
ND1 A:HIS198 2.4 24.6 1.0
CD A:GLU161 2.5 43.7 1.0
MN A:MN406 2.8 47.3 0.6
CD A:GLU93 2.9 31.3 1.0
CD A:GLU195 3.0 43.8 1.0
HB3 A:HIS198 3.3 23.1 1.0
OE2 A:GLU93 3.3 40.8 1.0
CG A:HIS198 3.3 26.8 1.0
HB2 A:HIS198 3.4 23.1 1.0
HA A:GLU195 3.4 29.3 1.0
CE1 A:HIS198 3.4 24.3 1.0
OE1 A:GLU195 3.4 47.0 1.0
CB A:HIS198 3.6 19.3 1.0
HE1 A:HIS198 3.6 29.1 1.0
HB3 A:GLU161 3.6 39.1 1.0
CG A:GLU161 3.9 41.8 1.0
HE21 A:GLN65 4.0 44.8 1.0
CG A:GLU93 4.1 25.3 1.0
HG2 A:GLU93 4.2 30.3 1.0
HE1 A:HIS96 4.3 25.8 1.0
HG3 A:GLN65 4.3 40.6 1.0
CB A:GLU161 4.3 32.6 1.0
CA A:GLU195 4.3 24.4 1.0
HG3 A:GLU161 4.3 50.1 1.0
HG3 A:GLU93 4.3 30.3 1.0
CG A:GLU195 4.3 36.1 1.0
HB3 A:GLU195 4.5 36.9 1.0
HG2 A:GLU161 4.5 50.1 1.0
NE2 A:HIS198 4.5 28.7 1.0
CD2 A:HIS198 4.5 27.1 1.0
CB A:GLU195 4.6 30.7 1.0
HB3 A:GLN65 4.6 35.3 1.0
HE3 A:MET89 4.6 25.9 1.0
HA A:GLU161 4.7 39.0 1.0
HG2 A:GLU195 4.7 43.3 1.0
NE2 A:GLN65 4.8 37.3 1.0
OD1 A:ASP62 4.9 36.6 1.0
CE1 A:HIS96 5.0 21.5 1.0
HG3 A:GLU195 5.0 43.3 1.0
HB2 A:GLU161 5.0 39.1 1.0

Iron binding site 2 out of 2 in 6tqz

Go back to Iron Binding Sites List in 6tqz
Iron 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 Iron with other atoms in the Fe 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:Fe401

b:49.8
occ:0.80
 OE1 B:GLU93 1.8 39.3 1.0
OE2 B:GLU195 2.0 52.2 1.0
OE1 B:GLU161 2.4 49.8 1.0
OE2 B:GLU161 2.4 46.7 1.0
ND1 B:HIS198 2.5 24.5 1.0
CD B:GLU161 2.6 55.9 1.0
CD B:GLU93 2.9 28.2 1.0
CD B:GLU195 2.9 40.3 1.0
MN B:MN404 3.1 41.8 0.5
OE1 B:GLU195 3.2 40.0 1.0
OE2 B:GLU93 3.3 46.7 1.0
HB2 B:HIS198 3.3 23.3 1.0
HB3 B:HIS198 3.4 23.3 1.0
CG B:HIS198 3.4 22.8 1.0
HA B:GLU195 3.4 29.8 1.0
CE1 B:HIS198 3.5 21.5 1.0
HB3 B:GLU161 3.5 46.9 1.0
CB B:HIS198 3.6 19.4 1.0
HE1 B:HIS198 3.7 25.8 1.0
CG B:GLU161 3.9 41.9 1.0
CG B:GLU93 4.1 28.7 1.0
HE21 B:GLN65 4.1 44.8 1.0
CB B:GLU161 4.2 39.1 1.0
HG2 B:GLU93 4.3 34.5 1.0
HE1 B:HIS96 4.3 30.0 1.0
CG B:GLU195 4.3 33.0 1.0
HG3 B:GLU93 4.3 34.5 1.0
HG3 B:GLU161 4.3 50.2 1.0
CA B:GLU195 4.3 24.8 1.0
HG3 B:GLN65 4.3 39.3 1.0
HG2 B:GLU161 4.5 50.2 1.0
HB3 B:GLU195 4.5 36.2 1.0
CD2 B:HIS198 4.6 19.6 1.0
NE2 B:HIS198 4.6 20.9 1.0
CB B:GLU195 4.6 30.2 1.0
HB3 B:GLN65 4.7 29.9 1.0
HA B:GLU161 4.7 41.8 1.0
HG2 B:GLU195 4.7 39.5 1.0
OD1 B:ASP62 4.8 33.7 1.0
HE3 B:MET89 4.8 27.4 1.0
HG3 B:GLU195 4.9 39.5 1.0
HB2 B:GLU161 4.9 46.9 1.0
HE2 B:PHE165 4.9 57.5 1.0
CE1 B:HIS96 5.0 30.0 1.0
NE2 B:GLN65 5.0 37.4 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 Dec 13 17:10:37 2020

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