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Iron in PDB 6qob: Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor

Enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor

All present enzymatic activity of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor:
1.17.4.1;

Protein crystallography data

The structure of Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor, PDB code: 6qob 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) 45.94 / 1.46
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 57.137, 60.377, 95.758, 90.00, 106.38, 90.00
R / Rfree (%) 17 / 19.4

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor (pdb code 6qob). 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 with Partially Oxidised Di-Iron Metallocofactor, PDB code: 6qob:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6qob

Go back to Iron Binding Sites List in 6qob
Iron binding site 1 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor


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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe402

b:15.9
occ:0.80
O A:HOH501 1.8 18.9 1.0
OE2 A:GLU161 1.9 12.9 0.5
OE1 A:GLU93 1.9 22.9 1.0
OE2 A:GLU195 2.1 34.6 1.0
OE2 A:GLU161 2.1 16.1 0.5
ND1 A:HIS198 2.2 15.3 1.0
O A:HOH511 2.3 22.3 1.0
OE1 A:GLU161 2.7 23.6 0.5
CD A:GLU161 2.7 19.3 0.5
CD A:GLU93 2.7 21.0 1.0
OE2 A:GLU93 2.9 28.5 1.0
CD A:GLU161 3.0 20.7 0.5
CE1 A:HIS198 3.1 19.1 1.0
CD A:GLU195 3.1 28.4 0.2
HG2 A:GLU161 3.2 16.6 0.5
HE1 A:HIS198 3.2 23.0 1.0
FE A:FE403 3.3 16.6 0.7
HA A:GLU195 3.3 18.4 1.0
CG A:HIS198 3.3 11.8 1.0
HB2 A:HIS198 3.5 16.2 1.0
OE1 A:GLU195 3.5 19.9 0.4
CG A:GLU161 3.6 13.8 0.5
HG2 A:GLN65 3.6 20.4 1.0
HB3 A:HIS198 3.6 16.2 1.0
CB A:HIS198 3.7 13.5 1.0
O A:HOH505 3.8 33.1 1.0
HB3 A:GLU161 3.9 17.2 0.5
OE1 A:GLU161 4.0 20.7 0.5
HE1 A:HIS96 4.0 18.7 1.0
HE2 A:PHE165 4.1 20.1 0.4
O A:HOH559 4.1 20.7 0.8
CG A:GLU93 4.1 15.0 1.0
CG A:GLU161 4.2 17.3 0.5
CA A:GLU195 4.3 15.3 1.0
NE2 A:HIS198 4.3 14.3 1.0
OD1 A:ASP62 4.3 16.9 0.4
CB A:GLU161 4.3 14.3 0.5
HG3 A:GLU161 4.4 16.6 0.5
HG3 A:GLU93 4.4 18.0 1.0
CG A:GLU195 4.4 24.5 0.7
CD2 A:HIS198 4.4 13.6 1.0
HB3 A:GLU161 4.4 20.2 0.5
HG2 A:GLU93 4.4 18.0 1.0
HE21 A:GLN65 4.5 26.9 1.0
HA A:GLU161 4.5 15.4 0.5
CG A:GLN65 4.5 17.0 1.0
HB2 A:GLU195 4.6 23.3 1.0
HG2 A:GLU161 4.6 20.8 0.5
CE1 A:HIS96 4.6 15.6 1.0
HG3 A:GLU161 4.6 20.8 0.5
HG3 A:GLN65 4.7 20.4 1.0
OD1 A:ASP62 4.7 15.5 0.6
CB A:GLU195 4.7 19.4 1.0
HG3 A:GLU195 4.7 29.4 0.6
ND1 A:HIS96 4.7 13.5 1.0
CE2 A:PHE165 4.7 16.8 0.3
HZ A:PHE165 4.8 29.4 1.0
CB A:GLU161 4.8 16.9 0.5
HA A:GLU161 4.8 16.7 0.5
HE3 A:MET89 4.8 24.1 1.0
N A:GLU195 4.9 14.5 1.0
OD2 A:ASP62 5.0 13.0 0.4

Iron binding site 2 out of 4 in 6qob

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Iron binding site 2 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor


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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe403

b:16.6
occ:0.72
O A:HOH559 1.9 20.7 0.8
OD2 A:ASP62 2.0 13.0 0.4
OE2 A:GLU93 2.0 28.5 1.0
ND1 A:HIS96 2.1 13.5 1.0
OD1 A:ASP62 2.1 15.5 0.6
O A:HOH501 2.2 18.9 1.0
CG A:ASP62 2.7 17.1 0.4
OD1 A:ASP62 2.8 16.9 0.4
CE1 A:HIS96 2.9 15.6 1.0
HE1 A:HIS96 3.0 18.7 1.0
O A:HOH511 3.0 22.3 1.0
CG A:ASP62 3.2 16.7 0.6
CD A:GLU93 3.2 21.0 1.0
CG A:HIS96 3.3 10.7 1.0
FE A:FE402 3.3 15.9 0.8
HA A:GLU93 3.3 13.1 1.0
OD2 A:ASP62 3.5 20.1 0.6
HB2 A:HIS96 3.5 13.4 1.0
HG23 A:ILE191 3.6 17.7 1.0
HB3 A:HIS96 3.7 13.4 1.0
OE1 A:GLU195 3.7 19.9 0.4
CB A:HIS96 3.7 11.2 1.0
OE1 A:GLU93 3.7 22.9 1.0
HZ A:PHE165 3.7 29.4 1.0
OE2 A:GLU195 3.9 34.6 1.0
CD A:GLU195 4.0 28.4 0.2
CB A:ASP62 4.1 15.8 0.4
CZ A:PHE165 4.1 24.5 1.0
NE2 A:HIS96 4.1 13.5 1.0
HE1 A:HIS198 4.1 23.0 1.0
CA A:GLU93 4.2 10.9 1.0
HB3 A:GLU93 4.2 15.3 1.0
HB3 A:ASP62 4.3 18.9 0.4
CD2 A:HIS96 4.3 15.0 1.0
CG A:GLU93 4.4 15.0 1.0
CG2 A:ILE191 4.4 14.8 1.0
HB2 A:ASP62 4.5 18.9 0.4
HA A:ASP62 4.5 15.5 0.6
CB A:GLU93 4.5 12.8 1.0
HB2 A:GLU195 4.5 23.3 1.0
CB A:ASP62 4.5 14.3 0.6
HG21 A:ILE191 4.5 17.7 1.0
HE2 A:PHE165 4.5 20.1 0.4
HG22 A:ILE191 4.6 17.7 1.0
CE2 A:PHE165 4.6 16.8 0.3
CE1 A:HIS198 4.7 19.1 1.0
ND1 A:HIS198 4.7 15.3 1.0
HB3 A:ASP62 4.7 17.1 0.6
CE1 A:PHE165 4.7 20.2 1.0
HA A:ASP62 4.8 15.5 0.4
HE1 A:PHE165 4.8 24.3 1.0
HA A:GLU195 4.9 18.4 1.0
HE2 A:HIS96 4.9 16.2 1.0
OE2 A:GLU161 4.9 16.1 0.5
HG2 A:GLU93 4.9 18.0 1.0
HG3 A:GLU93 5.0 18.0 1.0
O A:GLU93 5.0 11.9 1.0

Iron binding site 3 out of 4 in 6qob

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Iron binding site 3 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor


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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe405

b:15.8
occ:0.77
O B:HOH541 1.8 21.5 0.9
OE2 B:GLU93 2.1 25.8 1.0
OD1 B:ASP62 2.1 13.0 0.7
OD2 B:ASP62 2.1 16.6 0.3
ND1 B:HIS96 2.2 11.8 1.0
O B:HOH501 2.3 18.8 1.0
CG B:ASP62 2.7 16.3 0.3
OD1 B:ASP62 2.7 11.5 0.3
CE1 B:HIS96 3.0 12.9 1.0
HE1 B:HIS96 3.0 15.5 1.0
O B:HOH525 3.1 23.3 1.0
CG B:ASP62 3.2 19.5 0.7
CD B:GLU93 3.2 16.8 1.0
CG B:HIS96 3.3 10.2 1.0
HA B:GLU93 3.3 12.5 1.0
FE B:FE406 3.3 14.3 0.8
HB2 B:HIS96 3.5 12.5 1.0
HZ B:PHE165 3.5 28.9 1.0
HG23 B:ILE191 3.6 15.1 1.0
OD2 B:ASP62 3.6 19.5 0.7
HB3 B:HIS96 3.7 12.5 1.0
CB B:HIS96 3.7 10.4 1.0
OE1 B:GLU195 3.8 14.3 0.4
OE1 B:GLU93 3.8 21.5 1.0
OE2 B:GLU195 3.9 28.9 1.0
CZ B:PHE165 4.0 24.1 1.0
CD B:GLU195 4.1 14.5 0.3
CB B:ASP62 4.1 13.4 0.3
HE2 B:PHE165 4.1 44.9 1.0
NE2 B:HIS96 4.2 12.7 1.0
HB3 B:GLU93 4.2 13.4 1.0
HE1 B:HIS198 4.2 15.7 1.0
CA B:GLU93 4.2 10.4 1.0
HB3 B:ASP62 4.3 16.0 0.3
CE2 B:PHE165 4.3 37.4 1.0
CG2 B:ILE191 4.3 12.5 1.0
CD2 B:HIS96 4.3 13.3 1.0
CG B:GLU93 4.4 13.7 1.0
CB B:GLU93 4.4 11.1 1.0
HG22 B:ILE191 4.4 15.1 1.0
HA B:ASP62 4.5 14.8 0.7
CB B:ASP62 4.5 12.7 0.7
HB2 B:GLU195 4.5 19.1 1.0
HG21 B:ILE191 4.5 15.1 1.0
HB2 B:ASP62 4.5 16.0 0.3
HB3 B:ASP62 4.6 15.2 0.7
ND1 B:HIS198 4.7 15.3 1.0
CE1 B:HIS198 4.7 13.1 1.0
HA B:ASP62 4.7 14.9 0.3
CE1 B:PHE165 4.8 20.0 1.0
O B:GLU93 4.9 10.5 1.0
HE2 B:HIS96 4.9 15.3 1.0
HG2 B:GLU93 4.9 16.5 1.0
OE1 B:GLU161 4.9 14.4 0.5
HG3 B:GLU93 5.0 16.5 1.0
HA B:GLU195 5.0 17.6 1.0
HE1 B:PHE165 5.0 24.0 1.0

Iron binding site 4 out of 4 in 6qob

Go back to Iron Binding Sites List in 6qob
Iron binding site 4 out of 4 in the Crystal Structure of Ribonucleotide Reductase Nrdf From Bacillus Anthracis with Partially Oxidised Di-Iron Metallocofactor


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 with Partially Oxidised Di-Iron Metallocofactor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe406

b:14.3
occ:0.83
OE1 B:GLU93 1.9 21.5 1.0
OE1 B:GLU161 1.9 14.1 0.6
O B:HOH501 1.9 18.8 1.0
OE1 B:GLU161 2.0 14.4 0.5
OE2 B:GLU195 2.1 28.9 1.0
O B:HOH525 2.2 23.3 1.0
ND1 B:HIS198 2.3 15.3 1.0
CD B:GLU93 2.6 16.8 1.0
OE2 B:GLU93 2.8 25.8 1.0
CD B:GLU161 2.8 22.3 0.5
OE2 B:GLU161 2.9 25.9 0.5
CD B:GLU161 3.0 24.8 0.6
CD B:GLU195 3.1 14.5 0.3
CE1 B:HIS198 3.1 13.1 1.0
HG2 B:GLU161 3.2 14.8 0.6
HE1 B:HIS198 3.2 15.7 1.0
FE B:FE405 3.3 15.8 0.8
CG B:HIS198 3.3 13.1 1.0
HA B:GLU195 3.4 17.6 1.0
OE1 B:GLU195 3.5 14.3 0.4
HB2 B:HIS198 3.5 17.1 1.0
HB3 B:HIS198 3.6 17.1 1.0
CG B:GLU161 3.6 12.3 0.6
HG2 B:GLN65 3.6 22.0 1.0
HE2 B:PHE165 3.7 44.9 1.0
CB B:HIS198 3.7 14.2 1.0
HB3 B:GLU161 3.8 18.3 0.6
O B:HOH541 4.0 21.5 0.9
OE2 B:GLU161 4.0 23.0 0.6
O B:HOH503 4.0 29.5 1.0
CG B:GLU93 4.1 13.7 1.0
HE1 B:HIS96 4.1 15.5 1.0
OD1 B:ASP62 4.3 11.5 0.3
CG B:GLU161 4.3 13.9 0.5
CB B:GLU161 4.3 15.3 0.6
NE2 B:HIS198 4.3 11.9 1.0
CA B:GLU195 4.3 14.6 1.0
HG3 B:GLU93 4.3 16.5 1.0
HG2 B:GLU93 4.4 16.5 1.0
CG B:GLU195 4.4 16.8 0.6
HB3 B:GLU161 4.4 15.7 0.5
HG3 B:GLU161 4.4 14.8 0.6
CD2 B:HIS198 4.4 12.6 1.0
HE21 B:GLN65 4.5 30.0 1.0
CE2 B:PHE165 4.5 37.4 1.0
HA B:GLU161 4.5 17.1 0.5
HZ B:PHE165 4.5 28.9 1.0
CG B:GLN65 4.5 18.3 1.0
HB2 B:GLU195 4.6 19.1 1.0
HG3 B:GLU195 4.7 20.2 0.6
CB B:GLU195 4.7 15.9 1.0
HG3 B:GLN65 4.7 22.0 1.0
CE1 B:HIS96 4.7 12.9 1.0
OD1 B:ASP62 4.7 13.0 0.7
HG2 B:GLU161 4.7 16.6 0.5
HG3 B:GLU161 4.8 16.6 0.5
ND1 B:HIS96 4.8 11.8 1.0
HA B:GLU161 4.8 17.3 0.6
HE3 B:MET89 4.8 22.5 1.0
CB B:GLU161 4.8 13.1 0.5
CZ B:PHE165 4.9 24.1 1.0
N B:GLU195 5.0 12.7 1.0
HB2 B:GLU161 5.0 18.3 0.6

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 08:11:31 2024

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