Iron in PDB 2ozy: Crystal Structure of E.Coli Nrfb

The structure of Crystal Structure of E.Coli Nrfb, PDB code: 2ozy was solved by T.A.Clarke, D.J.Richardson, A.M.Hemmings, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.02 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.683, 59.668, 65.207, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.4

The binding sites of Iron atom in the Crystal Structure of E.Coli Nrfb (pdb code 2ozy). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of E.Coli Nrfb, PDB code: 2ozy:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Crystal Structure of E.Coli Nrfb


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 E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:10.1 occ:1.00 FE A:HEC201 0.0 10.1 1.0 ND A:HEC201 2.0 8.8 1.0 NC A:HEC201 2.0 9.7 1.0 NA A:HEC201 2.0 10.3 1.0 NB A:HEC201 2.0 10.6 1.0 NE2 A:HIS64 2.1 8.5 1.0 NE2 A:HIS28 2.1 7.7 1.0 CD2 A:HIS64 3.0 9.3 1.0 C4C A:HEC201 3.0 11.3 1.0 C1D A:HEC201 3.0 11.2 1.0 C1B A:HEC201 3.1 10.3 1.0 C4B A:HEC201 3.1 11.0 1.0 C4A A:HEC201 3.1 9.2 1.0 CE1 A:HIS28 3.1 7.7 1.0 C1A A:HEC201 3.1 9.1 1.0 C4D A:HEC201 3.1 11.3 1.0 C1C A:HEC201 3.1 9.2 1.0 CD2 A:HIS28 3.1 8.8 1.0 CE1 A:HIS64 3.2 10.8 1.0 CHD A:HEC201 3.4 10.7 1.0 CHB A:HEC201 3.4 10.3 1.0 CHA A:HEC201 3.4 10.5 1.0 CHC A:HEC201 3.4 10.8 1.0 CG A:HIS64 4.2 12.4 1.0 ND1 A:HIS28 4.2 8.6 1.0 ND1 A:HIS64 4.2 10.7 1.0 CG A:HIS28 4.3 7.4 1.0 C3C A:HEC201 4.3 11.0 1.0 C3B A:HEC201 4.3 11.1 1.0 C2B A:HEC201 4.3 11.5 1.0 C2D A:HEC201 4.3 11.6 1.0 C2C A:HEC201 4.3 10.2 1.0 C3A A:HEC201 4.3 9.6 1.0 C2A A:HEC201 4.3 11.7 1.0 C3D A:HEC201 4.3 11.8 1.0

Iron binding site 2 out of 5 in the Crystal Structure of E.Coli Nrfb


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 E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:6.2 occ:1.00 FE A:HEC202 0.0 6.2 1.0 NC A:HEC202 2.0 5.8 1.0 NA A:HEC202 2.0 4.8 1.0 ND A:HEC202 2.1 4.9 1.0 NB A:HEC202 2.1 4.8 1.0 NE2 A:HIS57 2.1 4.2 1.0 NE2 A:HIS120 2.1 9.9 1.0 C4C A:HEC202 3.0 6.9 1.0 C1A A:HEC202 3.0 6.0 1.0 C4D A:HEC202 3.0 3.4 1.0 C1C A:HEC202 3.1 7.2 1.0 C1D A:HEC202 3.1 6.0 1.0 CD2 A:HIS57 3.1 5.0 1.0 C4B A:HEC202 3.1 5.4 1.0 CD2 A:HIS120 3.1 6.7 1.0 C4A A:HEC202 3.1 5.2 1.0 CE1 A:HIS57 3.1 6.6 1.0 CE1 A:HIS120 3.1 8.7 1.0 C1B A:HEC202 3.1 5.7 1.0 CHA A:HEC202 3.4 5.6 1.0 CHD A:HEC202 3.4 6.0 1.0 CHC A:HEC202 3.4 5.3 1.0 CHB A:HEC202 3.5 6.7 1.0 ND1 A:HIS57 4.2 5.5 1.0 ND1 A:HIS120 4.2 7.9 1.0 CG A:HIS57 4.2 5.3 1.0 CG A:HIS120 4.2 6.5 1.0 C3C A:HEC202 4.2 6.2 1.0 C2A A:HEC202 4.3 9.0 1.0 C2C A:HEC202 4.3 5.7 1.0 C3D A:HEC202 4.3 5.7 1.0 C2D A:HEC202 4.3 5.5 1.0 C3A A:HEC202 4.3 7.7 1.0 C3B A:HEC202 4.3 8.0 1.0 C2B A:HEC202 4.3 6.9 1.0 CE A:MET35 5.0 10.7 1.0

Iron binding site 3 out of 5 in the Crystal Structure of E.Coli Nrfb


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 E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:6.5 occ:1.00 FE A:HEC203 0.0 6.5 1.0 NC A:HEC203 2.0 5.7 1.0 NB A:HEC203 2.0 4.3 1.0 NE2 A:HIS39 2.0 6.4 1.0 NA A:HEC203 2.1 6.0 1.0 ND A:HEC203 2.1 5.7 1.0 NE2 A:HIS92 2.1 4.9 1.0 CE1 A:HIS92 3.0 4.2 1.0 CE1 A:HIS39 3.0 5.9 1.0 CD2 A:HIS39 3.0 7.1 1.0 C4C A:HEC203 3.0 5.7 1.0 C1B A:HEC203 3.0 5.9 1.0 C1D A:HEC203 3.1 6.0 1.0 C4A A:HEC203 3.1 6.8 1.0 C4D A:HEC203 3.1 6.7 1.0 C1A A:HEC203 3.1 8.3 1.0 C1C A:HEC203 3.1 4.3 1.0 C4B A:HEC203 3.1 4.4 1.0 CD2 A:HIS92 3.2 5.6 1.0 CHD A:HEC203 3.4 4.4 1.0 CHB A:HEC203 3.4 5.8 1.0 CHA A:HEC203 3.4 6.5 1.0 CHC A:HEC203 3.5 5.4 1.0 ND1 A:HIS39 4.1 7.2 1.0 ND1 A:HIS92 4.1 4.5 1.0 CG A:HIS39 4.2 8.2 1.0 CG A:HIS92 4.3 4.2 1.0 C3C A:HEC203 4.3 4.8 1.0 C2B A:HEC203 4.3 5.2 1.0 C2D A:HEC203 4.3 7.5 1.0 C2A A:HEC203 4.3 9.2 1.0 C3A A:HEC203 4.3 7.4 1.0 C3D A:HEC203 4.3 9.6 1.0 C3B A:HEC203 4.3 3.6 1.0 C2C A:HEC203 4.3 4.2 1.0 CMA A:HEC204 5.0 5.8 1.0

Iron binding site 4 out of 5 in the Crystal Structure of E.Coli Nrfb


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 E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:6.4 occ:1.00 FE A:HEC204 0.0 6.4 1.0 NB A:HEC204 2.0 6.4 1.0 NE2 A:HIS104 2.0 4.1 1.0 NC A:HEC204 2.0 4.7 1.0 NA A:HEC204 2.1 7.0 1.0 ND A:HEC204 2.1 5.9 1.0 NE2 A:HIS117 2.1 5.3 1.0 CE1 A:HIS104 3.0 7.7 1.0 C4B A:HEC204 3.0 4.5 1.0 C1B A:HEC204 3.0 5.7 1.0 C1C A:HEC204 3.0 6.2 1.0 CE1 A:HIS117 3.1 7.3 1.0 CD2 A:HIS104 3.1 5.3 1.0 CD2 A:HIS117 3.1 6.5 1.0 C1A A:HEC204 3.1 7.5 1.0 C4A A:HEC204 3.1 6.3 1.0 C4D A:HEC204 3.1 6.2 1.0 C4C A:HEC204 3.1 6.2 1.0 C1D A:HEC204 3.1 5.2 1.0 CHC A:HEC204 3.4 5.5 1.0 CHA A:HEC204 3.4 7.3 1.0 CHB A:HEC204 3.4 6.1 1.0 CHD A:HEC204 3.4 7.0 1.0 ND1 A:HIS104 4.1 9.2 1.0 ND1 A:HIS117 4.2 5.8 1.0 CG A:HIS104 4.2 5.5 1.0 CG A:HIS117 4.2 5.6 1.0 C3B A:HEC204 4.2 5.8 1.0 C2B A:HEC204 4.2 6.5 1.0 C2A A:HEC204 4.3 8.0 1.0 C3A A:HEC204 4.3 7.0 1.0 C2C A:HEC204 4.3 6.0 1.0 C3C A:HEC204 4.3 6.5 1.0 C3D A:HEC204 4.3 7.0 1.0 C2D A:HEC204 4.3 7.7 1.0

Iron binding site 5 out of 5 in the Crystal Structure of E.Coli Nrfb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:7.3 occ:1.00 FE A:HEC205 0.0 7.3 1.0 NA A:HEC205 2.0 6.0 1.0 NB A:HEC205 2.0 5.8 1.0 NC A:HEC205 2.0 5.6 1.0 NE2 A:HIS142 2.0 10.2 1.0 NE2 A:HIS107 2.1 6.9 1.0 ND A:HEC205 2.1 5.9 1.0 CE1 A:HIS142 3.0 10.7 1.0 C1B A:HEC205 3.0 6.0 1.0 C1A A:HEC205 3.0 7.1 1.0 CE1 A:HIS107 3.0 8.9 1.0 CD2 A:HIS107 3.0 6.0 1.0 C4A A:HEC205 3.1 6.6 1.0 C4B A:HEC205 3.1 5.4 1.0 C4C A:HEC205 3.1 6.7 1.0 C1D A:HEC205 3.1 8.0 1.0 C4D A:HEC205 3.1 6.8 1.0 C1C A:HEC205 3.1 6.3 1.0 CD2 A:HIS142 3.1 8.3 1.0 CHB A:HEC205 3.4 6.6 1.0 CHA A:HEC205 3.4 6.7 1.0 CHD A:HEC205 3.4 7.1 1.0 CHC A:HEC205 3.5 6.7 1.0 ND1 A:HIS142 4.1 9.1 1.0 ND1 A:HIS107 4.1 9.2 1.0 CG A:HIS107 4.2 6.1 1.0 CG A:HIS142 4.2 7.7 1.0 C2B A:HEC205 4.2 6.0 1.0 C2A A:HEC205 4.3 9.4 1.0 C3B A:HEC205 4.3 5.9 1.0 C3A A:HEC205 4.3 6.6 1.0 C3C A:HEC205 4.3 4.2 1.0 C2C A:HEC205 4.3 5.2 1.0 C2D A:HEC205 4.3 9.8 1.0 C3D A:HEC205 4.3 8.7 1.0

T.A.Clarke, J.A.Cole, D.J.Richardson, A.M.Hemmings. The Crystal Structure of the Pentahaem C-Type Cytochrome Nrfb and Characterization of Its Solution-State Interaction with the Pentahaem Nitrite Reductase Nrfa. Biochem.J. V. 406 19 2007.
ISSN: ISSN 0264-6021
PubMed: 17521287
DOI: 10.1042/BJ20070321