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Iron in PDB 6qo7: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced):
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced), PDB code: 6qo7 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) 41.82 / 1.63
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.293, 59.958, 95.360, 90.00, 107.11, 90.00
R / Rfree (%) 15.9 / 19.2

Other elements in 6qo7:

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced) (pdb code 6qo7). 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 Aerobically Soaked with Ferrous Ions (Photo-Reduced), PDB code: 6qo7:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qo7

Go back to Iron Binding Sites List in 6qo7
Iron binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)


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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe401

b:15.3
occ:1.00
 OE1 A:GLU93 2.1 21.6 1.0
OE1 A:GLU161 2.1 22.6 1.0
ND1 A:HIS198 2.1 13.9 1.0
OE2 A:GLU195 2.1 18.6 1.0
OE2 A:GLU161 2.4 18.2 1.0
CD A:GLU161 2.5 19.2 1.0
CD A:GLU93 2.8 22.9 1.0
OE2 A:GLU93 2.9 19.9 1.0
CE1 A:HIS198 3.0 13.6 1.0
HE1 A:HIS198 3.1 16.3 1.0
HA A:GLU195 3.2 16.7 1.0
CG A:HIS198 3.2 13.9 1.0
HB2 A:HIS198 3.2 13.5 1.0
CD A:GLU195 3.2 25.4 1.0
HB3 A:HIS198 3.4 13.5 1.0
CB A:HIS198 3.5 11.3 1.0
HE2 A:PHE165 3.7 21.3 1.0
HG2 A:GLN65 3.7 26.0 1.0
FE A:FE2402 3.9 17.8 1.0
OE1 A:GLU195 3.9 20.6 1.0
CG A:GLU161 4.0 18.5 1.0
CA A:GLU195 4.1 13.9 1.0
HB3 A:GLU195 4.1 20.1 1.0
HE3 A:MET70 4.1 32.8 1.0
HE1 A:HIS96 4.1 20.5 1.0
NE2 A:HIS198 4.2 13.2 1.0
CG A:GLU93 4.2 15.4 1.0
HE21 A:GLN65 4.3 26.8 1.0
CD2 A:HIS198 4.3 14.7 1.0
CG A:GLU195 4.3 23.9 1.0
CB A:GLU195 4.3 16.8 1.0
HG2 A:GLU93 4.4 18.5 1.0
HB3 A:GLU161 4.4 17.3 1.0
HG3 A:GLU93 4.4 18.5 1.0
HG3 A:GLU161 4.4 22.2 1.0
HE2 A:MET70 4.5 32.8 1.0
HG2 A:GLU161 4.5 22.2 1.0
CE2 A:PHE165 4.5 17.7 1.0
HA A:GLU161 4.5 15.8 1.0
HZ A:PHE165 4.5 18.9 1.0
CG A:GLN65 4.6 21.7 1.0
CE A:MET70 4.7 27.3 1.0
CB A:GLU161 4.7 14.4 1.0
N A:GLU195 4.8 14.6 1.0
HG3 A:GLN65 4.9 26.0 1.0
CE1 A:HIS96 4.9 17.1 1.0
HG3 A:GLU195 4.9 28.6 1.0
HG2 A:GLU195 4.9 28.6 1.0
HE2 A:HIS198 4.9 15.9 1.0
HB3 A:MET89 4.9 15.0 1.0
CZ A:PHE165 4.9 15.8 1.0
O A:GLU195 5.0 13.7 1.0
HE1 A:MET70 5.0 32.8 1.0
CA A:HIS198 5.0 14.5 1.0
OD1 A:ASP62 5.0 19.7 1.0

Iron binding site 2 out of 4 in 6qo7

Go back to Iron Binding Sites List in 6qo7
Iron binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)


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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:17.8
occ:1.00
 OD1 A:ASP62 2.0 19.7 1.0
ND1 A:HIS96 2.0 14.1 1.0
OE1 A:GLU195 2.0 20.6 1.0
OE2 A:GLU93 2.2 19.9 1.0
CD A:GLU195 2.7 25.4 1.0
CG A:ASP62 2.8 14.4 1.0
OE2 A:GLU195 2.8 18.6 1.0
CE1 A:HIS96 2.9 17.1 1.0
HE1 A:HIS96 3.0 20.5 1.0
OD2 A:ASP62 3.0 20.6 1.0
HA A:GLU93 3.0 17.2 1.0
CD A:GLU93 3.1 22.9 1.0
CG A:HIS96 3.2 13.3 1.0
HB2 A:HIS96 3.3 18.5 1.0
HZ A:PHE165 3.5 18.9 1.0
HG23 A:ILE191 3.6 17.1 1.0
CB A:HIS96 3.6 15.4 1.0
HB3 A:HIS96 3.6 18.5 1.0
OE1 A:GLU93 3.7 21.6 1.0
FE A:FE2401 3.9 15.3 1.0
CA A:GLU93 3.9 14.3 1.0
O A:HOH501 3.9 39.0 1.0
CZ A:PHE165 4.0 15.8 1.0
HB3 A:GLU93 4.0 16.2 1.0
NE2 A:HIS96 4.0 13.8 1.0
CG A:GLU195 4.1 23.9 1.0
CD2 A:HIS96 4.2 13.5 1.0
CB A:ASP62 4.2 15.7 1.0
CG A:GLU93 4.2 15.4 1.0
CB A:GLU93 4.2 13.5 1.0
HA A:ASP62 4.3 16.0 1.0
CG2 A:ILE191 4.3 14.2 1.0
HG2 A:GLU195 4.3 28.6 1.0
HE2 A:PHE165 4.3 21.3 1.0
HE1 A:HIS198 4.4 16.3 1.0
HG3 A:GLU195 4.4 28.6 1.0
CE2 A:PHE165 4.4 17.7 1.0
HG21 A:ILE191 4.4 17.1 1.0
HB3 A:ASP62 4.4 18.9 1.0
HG22 A:ILE191 4.5 17.1 1.0
O A:GLU93 4.6 13.2 1.0
CE1 A:PHE165 4.7 13.6 1.0
HG2 A:GLU93 4.8 18.5 1.0
N A:GLU93 4.8 12.9 1.0
HH A:TYR100 4.8 40.0 1.0
HE1 A:PHE165 4.8 16.3 1.0
HE2 A:HIS96 4.8 16.6 1.0
C A:GLU93 4.8 13.4 1.0
CA A:ASP62 4.8 13.3 1.0
HG3 A:GLU93 4.8 18.5 1.0
HB2 A:ASP62 4.8 18.9 1.0
O A:MET92 4.8 12.7 1.0

Iron binding site 3 out of 4 in 6qo7

Go back to Iron Binding Sites List in 6qo7
Iron binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)


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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe401

b:16.1
occ:1.00
 OD1 B:ASP62 2.0 21.7 1.0
OE2 B:GLU195 2.1 20.9 1.0
ND1 B:HIS96 2.1 12.6 1.0
OE2 B:GLU93 2.2 18.9 1.0
CD B:GLU195 2.7 22.2 1.0
CG B:ASP62 2.8 20.2 1.0
OE1 B:GLU195 2.8 18.3 1.0
CE1 B:HIS96 2.9 13.5 1.0
OD2 B:ASP62 3.0 22.2 1.0
HA B:GLU93 3.0 14.3 1.0
HE1 B:HIS96 3.0 16.2 1.0
CD B:GLU93 3.1 17.1 1.0
CG B:HIS96 3.2 13.4 1.0
HB2 B:HIS96 3.3 19.1 1.0
HG23 B:ILE191 3.5 15.5 1.0
CB B:HIS96 3.6 15.9 1.0
HZ B:PHE165 3.6 22.4 1.0
HB3 B:HIS96 3.6 19.1 1.0
OE1 B:GLU93 3.7 21.5 1.0
CA B:GLU93 3.9 11.9 1.0
FE B:FE2402 3.9 14.5 1.0
O B:HOH502 3.9 29.9 1.0
HB3 B:GLU93 4.0 16.0 1.0
CZ B:PHE165 4.0 18.7 1.0
NE2 B:HIS96 4.1 12.8 1.0
CG B:GLU195 4.2 18.9 1.0
CB B:ASP62 4.2 14.5 1.0
CG B:GLU93 4.2 13.2 1.0
CB B:GLU93 4.2 13.3 1.0
CD2 B:HIS96 4.2 12.6 1.0
HA B:ASP62 4.3 17.5 1.0
HE2 B:PHE165 4.3 23.2 1.0
HE1 B:HIS198 4.3 14.1 1.0
CG2 B:ILE191 4.3 12.9 1.0
HG2 B:GLU195 4.4 22.7 1.0
HB3 B:ASP62 4.4 17.4 1.0
CE2 B:PHE165 4.4 19.3 1.0
HG3 B:GLU195 4.4 22.7 1.0
HG21 B:ILE191 4.5 15.5 1.0
HG22 B:ILE191 4.5 15.5 1.0
O B:GLU93 4.6 13.4 1.0
N B:GLU93 4.7 11.7 1.0
HG2 B:GLU93 4.8 15.9 1.0
C B:GLU93 4.8 15.9 1.0
HB2 B:ASP62 4.8 17.4 1.0
HG3 B:GLU93 4.8 15.9 1.0
CE1 B:PHE165 4.8 15.2 1.0
O B:MET92 4.8 12.0 1.0
CA B:ASP62 4.8 14.6 1.0
HE2 B:HIS96 4.8 15.4 1.0
HE1 B:PHE165 4.9 18.2 1.0
CE1 B:HIS198 4.9 11.8 1.0

Iron binding site 4 out of 4 in 6qo7

Go back to Iron Binding Sites List in 6qo7
Iron binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis Aerobically Soaked with Ferrous Ions (Photo-Reduced)


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 Aerobically Soaked with Ferrous Ions (Photo-Reduced) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe402

b:14.5
occ:1.00
 OE2 B:GLU161 2.0 22.3 1.0
OE1 B:GLU93 2.1 21.5 1.0
ND1 B:HIS198 2.1 12.6 1.0
OE1 B:GLU195 2.1 18.3 1.0
OE1 B:GLU161 2.4 20.6 1.0
CD B:GLU161 2.5 19.9 1.0
CD B:GLU93 2.8 17.1 1.0
OE2 B:GLU93 2.9 18.9 1.0
CE1 B:HIS198 3.1 11.8 1.0
HA B:GLU195 3.2 19.1 1.0
CG B:HIS198 3.2 13.8 1.0
HE1 B:HIS198 3.2 14.1 1.0
HB2 B:HIS198 3.2 14.0 1.0
CD B:GLU195 3.3 22.2 1.0
HB3 B:HIS198 3.4 14.0 1.0
CB B:HIS198 3.5 11.7 1.0
HE2 B:PHE165 3.6 23.2 1.0
HG2 B:GLN65 3.7 34.5 1.0
FE B:FE2401 3.9 16.1 1.0
OE2 B:GLU195 4.0 20.9 1.0
CG B:GLU161 4.0 17.4 1.0
HB3 B:GLU195 4.0 18.7 1.0
CA B:GLU195 4.0 15.9 1.0
CG B:GLU93 4.2 13.2 1.0
NE2 B:HIS198 4.2 12.1 1.0
HE1 B:HIS96 4.2 16.2 1.0
CD2 B:HIS198 4.3 12.6 1.0
HE21 B:GLN65 4.3 29.3 1.0
HE3 B:MET70 4.3 40.1 1.0
HE2 B:MET70 4.3 40.1 1.0
HB3 B:GLU161 4.3 16.0 1.0
CB B:GLU195 4.3 15.6 1.0
CG B:GLU195 4.3 18.9 1.0
CE2 B:PHE165 4.4 19.3 1.0
HG2 B:GLU93 4.4 15.9 1.0
HG3 B:GLU161 4.4 20.9 1.0
HG3 B:GLU93 4.4 15.9 1.0
HG2 B:GLU161 4.5 20.9 1.0
HA B:GLU161 4.5 18.2 1.0
HZ B:PHE165 4.5 22.4 1.0
CG B:GLN65 4.6 28.8 1.0
CB B:GLU161 4.6 13.3 1.0
CE B:MET70 4.7 33.4 1.0
N B:GLU195 4.8 13.1 1.0
HG3 B:GLN65 4.9 34.5 1.0
CZ B:PHE165 4.9 18.7 1.0
HG3 B:GLU195 4.9 22.7 1.0
OD1 B:ASP62 4.9 21.7 1.0
CE1 B:HIS96 4.9 13.5 1.0
HG2 B:GLU195 4.9 22.7 1.0
O B:GLU195 4.9 12.8 1.0
HE2 B:HIS198 5.0 14.6 1.0
HB3 B:MET89 5.0 14.7 1.0
HE1 B:MET70 5.0 40.1 1.0
O B:ASP194 5.0 14.6 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 08:09:10 2024

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