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

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

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically 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 Anaerobically Soaked with Fe(II) and Mn(II) Ions, PDB code: 6tqy 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) 41.56 / 1.77
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.247, 60.495, 95.996, 90.00, 106.53, 90.00
R / Rfree (%) 16.9 / 20.9

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically Soaked with Fe(II) and Mn(II) Ions (pdb code 6tqy). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically Soaked with Fe(II) and Mn(II) Ions, PDB code: 6tqy:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 6tqy

Go back to Manganese Binding Sites List in 6tqy
Manganese binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically 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 Anaerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:22.0
occ:0.85
 OD1 A:ASP62 2.0 30.4 1.0
O A:HOH567 2.1 28.8 1.0
OE1 A:GLU93 2.1 28.8 1.0
OE2 A:GLU195 2.2 23.3 1.0
OE2 A:GLU161 2.2 35.7 1.0
ND1 A:HIS96 2.3 19.3 1.0
CE1 A:HIS96 3.0 21.1 1.0
HE1 A:HIS96 3.0 25.4 1.0
CG A:ASP62 3.0 29.2 1.0
CD A:GLU195 3.2 33.9 1.0
CD A:GLU93 3.3 21.5 1.0
HA A:GLU93 3.3 20.8 1.0
CG A:HIS96 3.4 17.3 1.0
CD A:GLU161 3.4 37.1 1.0
OD2 A:ASP62 3.4 32.3 1.0
HG2 A:GLU195 3.5 44.8 1.0
MN A:MN402 3.5 26.5 1.0
HB2 A:HIS96 3.6 20.6 1.0
CG A:GLU195 3.7 37.4 1.0
HG3 A:GLU195 3.7 44.8 1.0
HG23 A:ILE191 3.8 24.3 1.0
HB3 A:HIS96 3.8 20.6 1.0
CB A:HIS96 3.9 17.2 1.0
HB3 A:GLU93 4.0 20.6 1.0
OE1 A:GLU161 4.1 43.0 1.0
OE2 A:GLU93 4.1 29.8 1.0
OE1 A:GLU195 4.2 28.2 1.0
CA A:GLU93 4.2 17.3 1.0
NE2 A:HIS96 4.2 18.7 1.0
HA A:ASP62 4.2 28.9 1.0
CB A:ASP62 4.3 23.1 1.0
CB A:GLU93 4.4 17.1 1.0
HE1 A:HIS198 4.4 26.7 1.0
CG A:GLU93 4.4 20.5 1.0
HG2 A:GLU161 4.4 49.6 1.0
CD2 A:HIS96 4.4 21.6 1.0
HB3 A:ASP62 4.5 27.7 1.0
CG2 A:ILE191 4.5 20.2 1.0
CG A:GLU161 4.6 41.3 1.0
HG21 A:ILE191 4.6 24.3 1.0
HG22 A:ILE191 4.6 24.3 1.0
ND1 A:HIS198 4.8 20.5 1.0
CA A:ASP62 4.8 24.1 1.0
CE1 A:HIS198 4.9 22.2 1.0
HB2 A:GLN65 4.9 29.2 1.0
HE2 A:HIS96 5.0 22.4 1.0
HG2 A:GLU93 5.0 24.6 1.0
O A:GLU93 5.0 19.3 1.0

Manganese binding site 2 out of 4 in 6tqy

Go back to Manganese Binding Sites List in 6tqy
Manganese binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically 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 Anaerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn402

b:26.5
occ:1.00
 OE2 A:GLU195 2.0 23.3 1.0
OE1 A:GLU161 2.1 43.0 1.0
OE1 A:GLU195 2.1 28.2 1.0
OE2 A:GLU93 2.1 29.8 1.0
ND1 A:HIS198 2.2 20.5 1.0
O A:HOH501 2.3 37.9 1.0
CD A:GLU195 2.3 33.9 1.0
OE1 A:GLU93 2.5 28.8 1.0
CD A:GLU161 2.6 37.1 1.0
CD A:GLU93 2.7 21.5 1.0
OE2 A:GLU161 2.8 35.7 1.0
CE1 A:HIS198 3.1 22.2 1.0
CG A:HIS198 3.2 18.5 1.0
HE1 A:HIS198 3.3 26.7 1.0
HB3 A:HIS198 3.3 21.6 1.0
HB2 A:HIS198 3.4 21.6 1.0
MN A:MN401 3.5 22.0 0.8
CB A:HIS198 3.6 18.0 1.0
HA A:GLU195 3.7 27.0 1.0
HE22 A:GLN65 3.8 43.8 1.0
HB3 A:GLU161 3.8 42.8 1.0
CG A:GLU195 3.8 37.4 1.0
CG A:GLU161 3.9 41.3 1.0
HB2 A:GLU161 4.0 42.8 1.0
HE1 A:HIS96 4.1 25.4 1.0
CB A:GLU161 4.1 35.6 1.0
CG A:GLU93 4.2 20.5 1.0
HG3 A:GLU195 4.2 44.8 1.0
HG2 A:GLU195 4.2 44.8 1.0
NE2 A:HIS198 4.3 19.2 1.0
HG3 A:GLN65 4.3 47.4 1.0
CD2 A:HIS198 4.3 19.2 1.0
HG2 A:GLU161 4.4 49.6 1.0
HG3 A:GLU161 4.5 49.6 1.0
HG2 A:GLU93 4.5 24.6 1.0
HE3 A:MET89 4.5 28.8 1.0
HG3 A:GLU93 4.5 24.6 1.0
CA A:GLU195 4.6 22.5 1.0
HB3 A:GLN65 4.6 29.2 1.0
NE2 A:GLN65 4.6 36.5 1.0
CB A:GLU195 4.7 25.9 1.0
O A:HOH567 4.7 28.8 1.0
CE1 A:HIS96 4.7 21.1 1.0
HB3 A:GLU195 4.8 31.1 1.0
HB3 A:MET89 4.9 19.9 1.0
ND1 A:HIS96 4.9 19.3 1.0
OD1 A:ASP62 4.9 30.4 1.0

Manganese binding site 3 out of 4 in 6tqy

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Manganese binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically 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 3 of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:20.1
occ:0.90
 OD1 B:ASP62 2.0 26.7 1.0
O B:HOH576 2.1 25.2 1.0
OE1 B:GLU93 2.1 23.0 1.0
OE2 B:GLU195 2.2 24.0 1.0
OE2 B:GLU161 2.2 32.9 1.0
ND1 B:HIS96 2.3 17.9 1.0
HE1 B:HIS96 3.0 22.7 1.0
CE1 B:HIS96 3.0 18.9 1.0
CG B:ASP62 3.1 24.6 1.0
CD B:GLU195 3.2 33.0 1.0
CD B:GLU93 3.3 21.9 1.0
HA B:GLU93 3.3 19.8 1.0
CD B:GLU161 3.4 30.3 1.0
CG B:HIS96 3.4 13.6 1.0
HG2 B:GLU195 3.5 40.2 1.0
OD2 B:ASP62 3.5 25.6 1.0
MN B:MN402 3.6 24.0 1.0
HB2 B:HIS96 3.6 19.0 1.0
CG B:GLU195 3.7 33.5 1.0
HG3 B:GLU195 3.7 40.2 1.0
HE1 B:PHE165 3.8 52.5 1.0
HG23 B:ILE191 3.8 21.2 1.0
HB3 B:HIS96 3.9 19.0 1.0
CB B:HIS96 3.9 15.8 1.0
OE2 B:GLU93 3.9 24.5 1.0
OE1 B:GLU161 4.0 32.2 1.0
HB3 B:GLU93 4.1 17.2 1.0
OE1 B:GLU195 4.2 25.6 1.0
NE2 B:HIS96 4.2 17.6 1.0
CA B:GLU93 4.2 16.5 1.0
HA B:ASP62 4.3 23.8 1.0
CB B:ASP62 4.4 18.4 1.0
HG2 B:GLU161 4.4 44.8 1.0
HE1 B:HIS198 4.4 21.7 1.0
CG B:GLU93 4.4 17.4 1.0
CD2 B:HIS96 4.4 18.6 1.0
CB B:GLU93 4.4 14.4 1.0
HB3 B:ASP62 4.5 22.1 1.0
CG B:GLU161 4.5 37.4 1.0
CE1 B:PHE165 4.5 43.8 1.0
CG2 B:ILE191 4.5 17.7 1.0
HG22 B:ILE191 4.6 21.2 1.0
HG21 B:ILE191 4.6 21.2 1.0
ND1 B:HIS198 4.8 19.0 1.0
CA B:ASP62 4.9 19.8 1.0
CE1 B:HIS198 4.9 18.1 1.0
HB2 B:GLN65 4.9 31.2 1.0
HE2 B:HIS96 4.9 21.2 1.0
HG3 B:GLN65 5.0 37.0 1.0
HG3 B:GLU93 5.0 20.9 1.0
O B:GLU93 5.0 16.7 1.0

Manganese binding site 4 out of 4 in 6tqy

Go back to Manganese Binding Sites List in 6tqy
Manganese binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically 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 4 of Crystal Structure of Ribonucleotide Reductase Nrdf L61G Variant From Bacillus Anthracis Anaerobically Soaked with Fe(II) and Mn(II) Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn402

b:24.0
occ:1.00
 OE2 B:GLU195 2.1 24.0 1.0
OE2 B:GLU93 2.1 24.5 1.0
OE1 B:GLU195 2.1 25.6 1.0
OE1 B:GLU161 2.1 32.2 1.0
O B:HOH504 2.2 32.4 1.0
ND1 B:HIS198 2.2 19.0 1.0
CD B:GLU195 2.4 33.0 1.0
CD B:GLU161 2.7 30.3 1.0
CD B:GLU93 2.9 21.9 1.0
OE2 B:GLU161 3.0 32.9 1.0
OE1 B:GLU93 3.0 23.0 1.0
HB3 B:HIS198 3.2 20.3 1.0
CE1 B:HIS198 3.2 18.1 1.0
CG B:HIS198 3.2 15.7 1.0
HB2 B:HIS198 3.4 20.3 1.0
HE1 B:HIS198 3.4 21.7 1.0
CB B:HIS198 3.5 16.9 1.0
MN B:MN401 3.6 20.1 0.9
HE21 B:GLN65 3.7 39.3 1.0
HA B:GLU195 3.7 25.7 1.0
HB3 B:GLU161 3.8 44.2 1.0
CG B:GLU195 3.9 33.5 1.0
CG B:GLU161 4.0 37.4 1.0
HB2 B:GLU161 4.0 44.2 1.0
HE1 B:HIS96 4.1 22.7 1.0
CB B:GLU161 4.2 36.9 1.0
HG3 B:GLU195 4.3 40.2 1.0
HG2 B:GLU195 4.3 40.2 1.0
NE2 B:HIS198 4.3 18.5 1.0
CG B:GLU93 4.3 17.4 1.0
CD2 B:HIS198 4.3 15.6 1.0
HE3 B:MET89 4.5 34.1 1.0
HG3 B:GLN65 4.5 37.0 1.0
NE2 B:GLN65 4.5 32.8 1.0
HG2 B:GLU161 4.5 44.8 1.0
HG3 B:GLU161 4.6 44.8 1.0
HG3 B:GLU93 4.6 20.9 1.0
HG2 B:GLU93 4.6 20.9 1.0
HB3 B:GLN65 4.6 31.2 1.0
CA B:GLU195 4.6 21.4 1.0
CB B:GLU195 4.7 22.7 1.0
HB3 B:GLU195 4.8 27.3 1.0
CE1 B:HIS96 4.8 18.9 1.0
HB3 B:MET89 4.9 18.1 1.0
O B:HOH576 4.9 25.2 1.0
HE22 B:GLN65 4.9 39.3 1.0
CA B:HIS198 5.0 16.4 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 Oct 6 07:12:21 2024

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