Iron in PDB 2p0b: Crystal Structure of Chemically-Reduced E.Coli Nrfb

The structure of Crystal Structure of Chemically-Reduced E.Coli Nrfb, PDB code: 2p0b 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)	7.99 / 1.74
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	49.727, 59.433, 65.318, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 19.2

The binding sites of Iron atom in the Crystal Structure of Chemically-Reduced E.Coli Nrfb (pdb code 2p0b). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Crystal Structure of Chemically-Reduced E.Coli Nrfb, PDB code: 2p0b:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Crystal Structure of Chemically-Reduced 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 Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:9.1 occ:1.00 FE A:HEC201 0.0 9.1 1.0 NA A:HEC201 2.0 6.0 1.0 NE2 A:HIS28 2.0 6.0 1.0 NC A:HEC201 2.0 8.2 1.0 ND A:HEC201 2.1 9.4 1.0 NB A:HEC201 2.1 7.9 1.0 NE2 A:HIS64 2.1 10.4 1.0 CE1 A:HIS28 2.9 7.9 1.0 CD2 A:HIS64 3.0 10.5 1.0 C4A A:HEC201 3.0 7.4 1.0 C4C A:HEC201 3.0 10.4 1.0 C1A A:HEC201 3.1 7.7 1.0 C1B A:HEC201 3.1 9.0 1.0 C1D A:HEC201 3.1 11.3 1.0 C1C A:HEC201 3.1 8.4 1.0 CD2 A:HIS28 3.1 9.3 1.0 C4D A:HEC201 3.1 8.9 1.0 C4B A:HEC201 3.2 8.9 1.0 CE1 A:HIS64 3.2 11.2 1.0 CHB A:HEC201 3.4 8.7 1.0 CHD A:HEC201 3.4 9.8 1.0 CHA A:HEC201 3.4 8.9 1.0 CHC A:HEC201 3.5 8.5 1.0 ND1 A:HIS28 4.1 8.0 1.0 CG A:HIS64 4.2 11.5 1.0 CG A:HIS28 4.2 7.9 1.0 ND1 A:HIS64 4.2 11.3 1.0 C3A A:HEC201 4.2 5.8 1.0 C3C A:HEC201 4.3 8.5 1.0 C2A A:HEC201 4.3 8.7 1.0 C2C A:HEC201 4.3 10.1 1.0 C2B A:HEC201 4.3 8.6 1.0 C2D A:HEC201 4.3 11.4 1.0 C3B A:HEC201 4.3 7.4 1.0 C3D A:HEC201 4.4 11.3 1.0

Iron binding site 2 out of 6 in the Crystal Structure of Chemically-Reduced 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 Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:4.2 occ:1.00 FE A:HEC202 0.0 4.2 1.0 NA A:HEC202 2.0 4.5 1.0 NC A:HEC202 2.0 4.2 1.0 NE2 A:HIS120 2.1 5.5 1.0 NB A:HEC202 2.1 2.6 1.0 ND A:HEC202 2.1 3.3 1.0 NE2 A:HIS57 2.1 2.5 1.0 CE1 A:HIS120 3.0 7.6 1.0 C1A A:HEC202 3.0 4.2 1.0 C4A A:HEC202 3.0 6.7 1.0 C4D A:HEC202 3.0 3.0 1.0 CD2 A:HIS57 3.0 2.6 1.0 C4B A:HEC202 3.1 2.9 1.0 CE1 A:HIS57 3.1 3.7 1.0 C1C A:HEC202 3.1 2.0 1.0 C4C A:HEC202 3.1 3.5 1.0 C1B A:HEC202 3.1 4.6 1.0 C1D A:HEC202 3.1 3.6 1.0 CD2 A:HIS120 3.1 5.6 1.0 CHA A:HEC202 3.3 4.4 1.0 CHC A:HEC202 3.4 3.3 1.0 CHB A:HEC202 3.4 5.2 1.0 CHD A:HEC202 3.4 3.3 1.0 ND1 A:HIS120 4.1 6.0 1.0 ND1 A:HIS57 4.2 2.7 1.0 CG A:HIS57 4.2 3.1 1.0 CG A:HIS120 4.2 5.4 1.0 C2A A:HEC202 4.2 7.5 1.0 C3A A:HEC202 4.2 5.6 1.0 C3B A:HEC202 4.3 4.7 1.0 C3D A:HEC202 4.3 2.9 1.0 C3C A:HEC202 4.3 2.6 1.0 C2B A:HEC202 4.3 3.8 1.0 C2C A:HEC202 4.3 2.0 1.0 C2D A:HEC202 4.3 3.3 1.0 CE A:MET35 4.9 7.6 1.0

Iron binding site 3 out of 6 in the Crystal Structure of Chemically-Reduced 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 Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:4.9 occ:1.00 FE A:HEC203 0.0 4.9 1.0 NB A:HEC203 2.0 3.0 1.0 NC A:HEC203 2.1 3.8 1.0 NE2 A:HIS39 2.1 5.3 1.0 NA A:HEC203 2.1 3.2 1.0 ND A:HEC203 2.1 4.0 1.0 NE2 A:HIS92 2.1 4.8 1.0 CE1 A:HIS39 3.0 3.9 1.0 CE1 A:HIS92 3.0 3.8 1.0 C1B A:HEC203 3.0 3.3 1.0 C4B A:HEC203 3.0 3.8 1.0 C1A A:HEC203 3.0 3.3 1.0 C4C A:HEC203 3.1 3.1 1.0 C1D A:HEC203 3.1 5.3 1.0 C4D A:HEC203 3.1 4.5 1.0 C1C A:HEC203 3.1 3.0 1.0 C4A A:HEC203 3.1 2.2 1.0 CD2 A:HIS39 3.1 6.7 1.0 CD2 A:HIS92 3.1 4.0 1.0 CHA A:HEC203 3.4 4.5 1.0 CHD A:HEC203 3.4 4.8 1.0 CHB A:HEC203 3.4 3.1 1.0 CHC A:HEC203 3.4 3.2 1.0 ND1 A:HIS39 4.1 4.8 1.0 ND1 A:HIS92 4.2 3.5 1.0 CG A:HIS39 4.2 6.6 1.0 CG A:HIS92 4.2 3.3 1.0 C2B A:HEC203 4.2 3.2 1.0 C3B A:HEC203 4.3 2.0 1.0 C2A A:HEC203 4.3 4.3 1.0 C3C A:HEC203 4.3 2.8 1.0 C2C A:HEC203 4.3 2.4 1.0 C3A A:HEC203 4.3 3.4 1.0 C3D A:HEC203 4.3 8.1 1.0 C2D A:HEC203 4.3 7.2 1.0 CBC A:HEC202 5.0 5.6 1.0

Iron binding site 4 out of 6 in the Crystal Structure of Chemically-Reduced 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 Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe204 b:3.6 occ:1.00 FE A:HEC204 0.0 3.6 1.0 NB A:HEC204 2.0 2.7 1.0 NE2 A:HIS104 2.0 2.1 1.0 NC A:HEC204 2.0 2.0 1.0 NA A:HEC204 2.1 3.8 1.0 NE2 A:HIS117 2.1 3.8 1.0 ND A:HEC204 2.1 2.0 1.0 CD2 A:HIS104 3.0 2.0 1.0 CE1 A:HIS117 3.0 4.1 1.0 C4B A:HEC204 3.0 2.1 1.0 CE1 A:HIS104 3.0 2.6 1.0 C1B A:HEC204 3.0 2.3 1.0 C1C A:HEC204 3.1 3.4 1.0 CD2 A:HIS117 3.1 3.3 1.0 C1A A:HEC204 3.1 4.1 1.0 C4A A:HEC204 3.1 3.1 1.0 C4C A:HEC204 3.1 2.9 1.0 C1D A:HEC204 3.1 2.0 1.0 C4D A:HEC204 3.1 2.8 1.0 CHC A:HEC204 3.4 3.4 1.0 CHB A:HEC204 3.4 4.5 1.0 CHA A:HEC204 3.4 4.6 1.0 CHD A:HEC204 3.4 4.4 1.0 ND1 A:HIS104 4.1 5.3 1.0 ND1 A:HIS117 4.2 2.9 1.0 CG A:HIS104 4.2 3.3 1.0 CG A:HIS117 4.2 2.0 1.0 C3B A:HEC204 4.3 2.8 1.0 C2B A:HEC204 4.3 4.3 1.0 C3A A:HEC204 4.3 4.8 1.0 C2A A:HEC204 4.3 5.0 1.0 C2C A:HEC204 4.3 2.1 1.0 C3C A:HEC204 4.3 3.1 1.0 C3D A:HEC204 4.3 4.1 1.0 C2D A:HEC204 4.3 4.4 1.0 O A:HOH289 4.9 21.6 1.0

Iron binding site 5 out of 6 in the Crystal Structure of Chemically-Reduced 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 Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:2.8 occ:0.50 FE A:HEC205 0.0 2.8 0.5 FE A:HEC205 0.3 3.9 0.5 ND A:HEC205 1.9 3.3 0.5 NA A:HEC205 2.0 3.4 0.5 NE2 A:HIS142 2.0 2.3 1.0 ND A:HEC205 2.0 2.0 0.5 NC A:HEC205 2.0 2.3 0.5 NB A:HEC205 2.1 2.0 0.5 NA A:HEC205 2.1 2.0 0.5 NE2 A:HIS107 2.1 3.9 1.0 NC A:HEC205 2.2 3.8 0.5 NB A:HEC205 2.2 3.3 0.5 C4D A:HEC205 2.9 4.5 0.5 CE1 A:HIS142 2.9 5.4 1.0 C1A A:HEC205 2.9 3.2 0.5 C1D A:HEC205 2.9 3.5 0.5 C4D A:HEC205 3.0 3.5 0.5 C1A A:HEC205 3.0 2.0 0.5 CE1 A:HIS107 3.0 6.8 1.0 C1D A:HEC205 3.0 2.5 0.5 C1C A:HEC205 3.1 2.0 0.5 C4A A:HEC205 3.1 3.2 0.5 C4B A:HEC205 3.1 2.0 0.5 C4C A:HEC205 3.1 2.2 0.5 CD2 A:HIS107 3.1 6.0 1.0 C1B A:HEC205 3.1 2.0 0.5 CD2 A:HIS142 3.1 3.1 1.0 C4A A:HEC205 3.1 2.0 0.5 C4C A:HEC205 3.1 3.8 0.5 C1B A:HEC205 3.2 3.3 0.5 CHA A:HEC205 3.2 3.9 0.5 C1C A:HEC205 3.2 2.8 0.5 C4B A:HEC205 3.2 3.6 0.5 CHA A:HEC205 3.4 2.1 0.5 CHD A:HEC205 3.4 4.1 0.5 CHC A:HEC205 3.4 2.0 0.5 CHD A:HEC205 3.4 2.6 0.5 CHB A:HEC205 3.5 2.3 0.5 CHB A:HEC205 3.5 3.9 0.5 CHC A:HEC205 3.6 3.0 0.5 ND1 A:HIS142 4.1 4.6 1.0 C3D A:HEC205 4.1 4.3 0.5 C2D A:HEC205 4.1 3.6 0.5 ND1 A:HIS107 4.2 7.8 1.0 CG A:HIS142 4.2 2.2 1.0 C2A A:HEC205 4.2 4.7 0.5 CG A:HIS107 4.2 4.9 1.0 C3D A:HEC205 4.2 2.5 0.5 C3A A:HEC205 4.2 3.7 0.5 C2D A:HEC205 4.3 2.7 0.5 C2A A:HEC205 4.3 3.0 0.5 C2C A:HEC205 4.3 2.0 0.5 C3C A:HEC205 4.3 2.0 0.5 C3B A:HEC205 4.3 2.0 0.5 C3A A:HEC205 4.3 2.0 0.5 C2B A:HEC205 4.3 2.1 0.5 C3C A:HEC205 4.4 2.9 0.5 C2B A:HEC205 4.4 3.4 0.5 C2C A:HEC205 4.4 3.0 0.5 C3B A:HEC205 4.5 3.5 0.5 NE2 A:GLN145 4.8 5.4 1.0

Iron binding site 6 out of 6 in the Crystal Structure of Chemically-Reduced E.Coli Nrfb


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Chemically-Reduced E.Coli Nrfb within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe205 b:3.9 occ:0.50 FE A:HEC205 0.0 3.9 0.5 FE A:HEC205 0.3 2.8 0.5 NB A:HEC205 1.8 2.0 0.5 NC A:HEC205 1.9 2.3 0.5 NE2 A:HIS107 1.9 3.9 1.0 NB A:HEC205 2.0 3.3 0.5 NC A:HEC205 2.0 3.8 0.5 ND A:HEC205 2.1 3.3 0.5 NA A:HEC205 2.1 3.4 0.5 NE2 A:HIS142 2.2 2.3 1.0 NA A:HEC205 2.2 2.0 0.5 ND A:HEC205 2.3 2.0 0.5 C4B A:HEC205 2.8 2.0 0.5 CE1 A:HIS107 2.8 6.8 1.0 C1C A:HEC205 2.8 2.0 0.5 C1B A:HEC205 3.0 2.0 0.5 C4B A:HEC205 3.0 3.6 0.5 C1C A:HEC205 3.0 2.8 0.5 CD2 A:HIS107 3.0 6.0 1.0 C4C A:HEC205 3.0 2.2 0.5 C1B A:HEC205 3.0 3.3 0.5 C4C A:HEC205 3.1 3.8 0.5 C1D A:HEC205 3.1 3.5 0.5 C4D A:HEC205 3.1 4.5 0.5 C4A A:HEC205 3.1 3.2 0.5 CHC A:HEC205 3.1 2.0 0.5 CE1 A:HIS142 3.2 5.4 1.0 C1A A:HEC205 3.2 3.2 0.5 CD2 A:HIS142 3.2 3.1 1.0 C4A A:HEC205 3.2 2.0 0.5 C1D A:HEC205 3.2 2.5 0.5 C1A A:HEC205 3.3 2.0 0.5 C4D A:HEC205 3.3 3.5 0.5 CHC A:HEC205 3.3 3.0 0.5 CHD A:HEC205 3.4 4.1 0.5 CHB A:HEC205 3.5 3.9 0.5 CHB A:HEC205 3.5 2.3 0.5 CHD A:HEC205 3.5 2.6 0.5 CHA A:HEC205 3.5 3.9 0.5 CHA A:HEC205 3.7 2.1 0.5 ND1 A:HIS107 4.0 7.8 1.0 C3B A:HEC205 4.0 2.0 0.5 C2C A:HEC205 4.1 2.0 0.5 CG A:HIS107 4.1 4.9 1.0 C2B A:HEC205 4.1 2.1 0.5 C3C A:HEC205 4.2 2.0 0.5 C3B A:HEC205 4.2 3.5 0.5 C2B A:HEC205 4.2 3.4 0.5 C2C A:HEC205 4.2 3.0 0.5 C3C A:HEC205 4.3 2.9 0.5 ND1 A:HIS142 4.3 4.6 1.0 CG A:HIS142 4.3 2.2 1.0 C2D A:HEC205 4.3 3.6 0.5 C3D A:HEC205 4.4 4.3 0.5 C3A A:HEC205 4.4 3.7 0.5 C2A A:HEC205 4.4 4.7 0.5 C3A A:HEC205 4.5 2.0 0.5 C2D A:HEC205 4.5 2.7 0.5 C2A A:HEC205 4.5 3.0 0.5 C3D A:HEC205 4.5 2.5 0.5

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