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Iron in PDB 6qo8: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions, PDB code: 6qo8 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) 45.90 / 1.32
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.558, 61.456, 95.794, 90.00, 106.59, 90.00
R / Rfree (%) 13.4 / 16.1

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions (pdb code 6qo8). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions, PDB code: 6qo8:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qo8

Go back to Iron Binding Sites List in 6qo8
Iron binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous 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 From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:7.8
occ:1.00
 OD1 A:ASP62 1.9 11.0 1.0
OE2 A:GLU195 2.0 11.2 1.0
OE2 A:GLU93 2.0 10.4 1.0
ND1 A:HIS96 2.1 9.6 1.0
CG A:ASP62 2.7 10.2 1.0
CD A:GLU195 2.8 9.6 1.0
OD2 A:ASP62 2.9 12.1 1.0
CD A:GLU93 3.0 9.3 1.0
CE1 A:HIS96 3.0 10.3 1.0
HA A:GLU93 3.0 9.2 1.0
OE1 A:GLU195 3.0 11.3 1.0
HE1 A:HIS96 3.1 12.3 1.0
CG A:HIS96 3.2 8.9 1.0
HB2 A:HIS96 3.2 11.0 1.0
HZ A:PHE165 3.5 13.7 1.0
OE1 A:GLU93 3.5 11.4 1.0
HG23 A:ILE191 3.5 13.2 1.0
CB A:HIS96 3.6 9.2 1.0
HB3 A:HIS96 3.6 11.0 1.0
HB3 A:GLU93 3.9 10.2 1.0
CA A:GLU93 3.9 7.7 1.0
FE A:FE2402 3.9 7.8 1.0
CZ A:PHE165 4.0 11.4 1.0
CG A:GLU93 4.1 8.9 1.0
CB A:GLU93 4.1 8.5 1.0
NE2 A:HIS96 4.1 10.5 1.0
CB A:ASP62 4.1 9.7 1.0
CG A:GLU195 4.2 10.6 1.0
HA A:ASP62 4.2 10.9 1.0
CD2 A:HIS96 4.2 10.0 1.0
HE1 A:HIS198 4.3 11.8 1.0
CG2 A:ILE191 4.3 11.0 1.0
HB3 A:ASP62 4.3 11.6 1.0
HG2 A:GLU195 4.4 12.7 1.0
HG21 A:ILE191 4.4 13.2 1.0
HE2 A:PHE165 4.4 12.9 1.0
HG3 A:GLU195 4.5 12.7 1.0
CE2 A:PHE165 4.5 10.8 1.0
HG22 A:ILE191 4.5 13.2 1.0
HH A:TYR100 4.6 13.7 0.7
O A:GLU93 4.6 9.3 1.0
HG3 A:GLU93 4.6 10.7 1.0
HG2 A:GLU93 4.6 10.7 1.0
CE1 A:PHE165 4.7 11.8 1.0
N A:GLU93 4.7 8.5 1.0
HE1 A:PHE165 4.7 14.1 1.0
O A:MET92 4.8 8.8 1.0
C A:GLU93 4.8 8.9 1.0
CA A:ASP62 4.8 9.1 1.0
HB2 A:ASP62 4.8 11.6 1.0
HE2 A:HIS96 4.9 12.6 1.0
CE1 A:HIS198 4.9 9.8 1.0

Iron binding site 2 out of 4 in 6qo8

Go back to Iron Binding Sites List in 6qo8
Iron binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous 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 From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:7.8
occ:1.00
 OE1 A:GLU93 2.0 11.4 1.0
OE1 A:GLU161 2.0 10.7 1.0
OE1 A:GLU195 2.0 11.3 1.0
ND1 A:HIS198 2.1 9.7 1.0
OE2 A:GLU161 2.5 11.6 1.0
CD A:GLU161 2.6 9.8 1.0
CD A:GLU93 2.8 9.3 1.0
CE1 A:HIS198 3.0 9.8 1.0
OE2 A:GLU93 3.0 10.4 1.0
CG A:HIS198 3.1 9.0 1.0
HA A:GLU195 3.1 11.2 1.0
CD A:GLU195 3.1 9.6 1.0
HE1 A:HIS198 3.1 11.8 1.0
HB2 A:HIS198 3.2 11.8 1.0
HB3 A:HIS198 3.4 11.8 1.0
CB A:HIS198 3.5 9.9 1.0
HG2 A:GLN65 3.7 13.7 1.0
HE2 A:PHE165 3.7 12.9 1.0
OE2 A:GLU195 3.8 11.2 1.0
FE A:FE2401 3.9 7.8 1.0
CA A:GLU195 4.0 9.3 1.0
CG A:GLU161 4.0 10.2 1.0
HB3 A:GLU195 4.1 11.7 1.0
CG A:GLU93 4.1 8.9 1.0
NE2 A:HIS198 4.1 10.5 1.0
HE3 A:MET70 4.1 16.4 1.0
CD2 A:HIS198 4.2 10.0 1.0
CG A:GLU195 4.2 10.6 1.0
HE21 A:GLN65 4.3 15.4 1.0
HE1 A:HIS96 4.3 12.3 1.0
CB A:GLU195 4.3 9.7 1.0
HG2 A:GLU93 4.3 10.7 1.0
HG3 A:GLU93 4.3 10.7 1.0
HB3 A:GLU161 4.4 11.7 1.0
HG3 A:GLU161 4.4 12.2 1.0
HZ A:PHE165 4.5 13.7 1.0
HE2 A:MET70 4.5 16.4 1.0
CE2 A:PHE165 4.5 10.8 1.0
HA A:GLU161 4.5 10.9 1.0
HG2 A:GLU161 4.5 12.2 1.0
CG A:GLN65 4.6 11.4 1.0
HG3 A:GLN65 4.7 13.7 1.0
HG3 A:GLU195 4.7 12.7 1.0
N A:GLU195 4.7 9.9 1.0
CE A:MET70 4.7 13.7 1.0
CB A:GLU161 4.7 9.8 1.0
HG2 A:GLU195 4.9 12.7 1.0
CZ A:PHE165 4.9 11.4 1.0
HE2 A:HIS198 4.9 12.6 1.0
OD1 A:ASP62 4.9 11.0 1.0
O A:GLU195 4.9 10.3 1.0
CE1 A:HIS96 5.0 10.3 1.0
HB3 A:MET89 5.0 10.3 1.0
O A:ASP194 5.0 10.1 1.0
CA A:HIS198 5.0 9.7 1.0
C A:GLU195 5.0 10.3 1.0

Iron binding site 3 out of 4 in 6qo8

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Iron binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:7.6
occ:1.00
 OE1 B:GLU93 2.0 11.4 1.0
OE1 B:GLU161 2.0 10.9 1.0
OE1 B:GLU195 2.1 11.6 1.0
ND1 B:HIS198 2.1 9.5 1.0
OE2 B:GLU161 2.5 12.2 1.0
CD B:GLU161 2.6 10.2 1.0
CD B:GLU93 2.8 9.0 1.0
OE2 B:GLU93 3.0 9.5 1.0
CE1 B:HIS198 3.0 10.2 1.0
CG B:HIS198 3.1 8.8 1.0
CD B:GLU195 3.1 9.2 1.0
HA B:GLU195 3.2 11.3 1.0
HE1 B:HIS198 3.2 12.2 1.0
HB2 B:HIS198 3.2 10.7 1.0
HB3 B:HIS198 3.4 10.7 1.0
CB B:HIS198 3.5 8.9 1.0
HE2 B:PHE165 3.7 13.3 1.0
HG2 B:GLN65 3.7 14.1 1.0
OE2 B:GLU195 3.8 10.7 1.0
FE B:FE2403 3.9 7.5 1.0
CA B:GLU195 4.0 9.4 1.0
CG B:GLU161 4.1 10.3 1.0
HB3 B:GLU195 4.1 11.1 1.0
NE2 B:HIS198 4.1 9.6 1.0
CG B:GLU93 4.1 9.6 1.0
CD2 B:HIS198 4.2 9.2 1.0
HE3 B:MET70 4.2 16.7 1.0
CG B:GLU195 4.2 9.5 1.0
HE21 B:GLN65 4.3 15.9 1.0
HE1 B:HIS96 4.3 11.7 1.0
CB B:GLU195 4.3 9.3 1.0
HG3 B:GLU93 4.3 11.5 1.0
HG2 B:GLU93 4.4 11.5 1.0
HB3 B:GLU161 4.4 11.7 1.0
HE2 B:MET70 4.4 16.7 1.0
HZ B:PHE165 4.4 13.0 1.0
CE2 B:PHE165 4.5 11.1 1.0
HA B:GLU161 4.5 10.3 1.0
HG3 B:GLU161 4.5 12.3 1.0
HG2 B:GLU161 4.5 12.3 1.0
CG B:GLN65 4.6 11.7 1.0
HG3 B:GLN65 4.7 14.1 1.0
HG3 B:GLU195 4.7 11.4 1.0
CB B:GLU161 4.7 9.8 1.0
N B:GLU195 4.8 9.3 1.0
CE B:MET70 4.8 13.9 1.0
CZ B:PHE165 4.9 10.9 1.0
OD1 B:ASP62 4.9 11.2 1.0
HG2 B:GLU195 4.9 11.4 1.0
HE2 B:HIS198 4.9 11.5 1.0
O B:GLU195 4.9 10.1 1.0
HB3 B:MET89 5.0 10.2 1.0
O B:ASP194 5.0 9.4 1.0
CA B:HIS198 5.0 8.9 1.0
CE1 B:HIS96 5.0 9.8 1.0

Iron binding site 4 out of 4 in 6qo8

Go back to Iron Binding Sites List in 6qo8
Iron binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Anaerobically Soaked with Ferrous Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe403

b:7.5
occ:1.00
 OD1 B:ASP62 1.9 11.2 1.0
OE2 B:GLU195 2.0 10.7 1.0
OE2 B:GLU93 2.0 9.5 1.0
ND1 B:HIS96 2.1 8.9 1.0
CG B:ASP62 2.7 9.6 1.0
CD B:GLU195 2.8 9.2 1.0
OD2 B:ASP62 2.9 11.8 1.0
HA B:GLU93 2.9 9.9 1.0
CE1 B:HIS96 2.9 9.8 1.0
CD B:GLU93 3.0 9.0 1.0
HE1 B:HIS96 3.0 11.7 1.0
OE1 B:GLU195 3.0 11.6 1.0
CG B:HIS96 3.2 8.2 1.0
HB2 B:HIS96 3.3 11.0 1.0
HZ B:PHE165 3.5 13.0 1.0
OE1 B:GLU93 3.5 11.4 1.0
HG23 B:ILE191 3.6 12.2 1.0
CB B:HIS96 3.6 9.1 1.0
HB3 B:HIS96 3.6 11.0 1.0
CA B:GLU93 3.8 8.2 1.0
HB3 B:GLU93 3.8 10.4 1.0
FE B:FE2402 3.9 7.6 1.0
CZ B:PHE165 4.0 10.9 1.0
CG B:GLU93 4.1 9.6 1.0
NE2 B:HIS96 4.1 9.6 1.0
CB B:GLU93 4.1 8.7 1.0
CB B:ASP62 4.1 9.4 1.0
CG B:GLU195 4.2 9.5 1.0
HA B:ASP62 4.2 10.9 1.0
CD2 B:HIS96 4.2 9.6 1.0
HE1 B:HIS198 4.3 12.2 1.0
HB3 B:ASP62 4.3 11.3 1.0
CG2 B:ILE191 4.3 10.2 1.0
HG2 B:GLU195 4.4 11.4 1.0
HG3 B:GLU195 4.4 11.4 1.0
HE2 B:PHE165 4.4 13.3 1.0
HG21 B:ILE191 4.5 12.2 1.0
CE2 B:PHE165 4.5 11.1 1.0
HG22 B:ILE191 4.5 12.2 1.0
HH B:TYR100 4.6 13.6 0.6
O B:GLU93 4.6 9.3 1.0
HG2 B:GLU93 4.7 11.5 1.0
N B:GLU93 4.7 8.0 1.0
HG3 B:GLU93 4.7 11.5 1.0
CE1 B:PHE165 4.7 12.0 1.0
C B:GLU93 4.7 8.5 1.0
HE1 B:PHE165 4.8 14.4 1.0
O B:MET92 4.8 8.9 1.0
HB2 B:ASP62 4.8 11.3 1.0
CA B:ASP62 4.8 9.1 1.0
HE2 B:HIS96 4.9 11.5 1.0
CE1 B:HIS198 4.9 10.2 1.0
ND1 B:HIS198 5.0 9.5 1.0

Reference:

K.Grave, W.Lambert, G.Berggren, J.J.Griese, M.D.Bennett, D.T.Logan, M.Hogbom. Redox-Induced Structural Changes in the Di-Iron and Di-Manganese Forms of Bacillus Anthracis Ribonucleotide Reductase Subunit Nrdf Suggest A Mechanism For Gating of Radical Access. J.Biol.Inorg.Chem. V. 24 849 2019.
ISSN: ESSN 1432-1327
PubMed: 31410573
DOI: 10.1007/S00775-019-01703-Z
Page generated: Wed Aug 7 08:10:37 2024

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