Iron in PDB 7o8d: Dife-Sulerythrin Oxidised By H2O2

The structure of Dife-Sulerythrin Oxidised By H2O2, PDB code: 7o8d was solved by J.-H.Jeoung, H.Dobbek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.96 / 1.12
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	71.971, 71.971, 99.814, 90, 90, 120
R / Rfree (%)	13.7 / 16.9

The structure of Dife-Sulerythrin Oxidised By H2O2 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Iron atom in the Dife-Sulerythrin Oxidised By H2O2 (pdb code 7o8d). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Dife-Sulerythrin Oxidised By H2O2, PDB code: 7o8d:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Dife-Sulerythrin Oxidised By H2O2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dife-Sulerythrin Oxidised By H2O2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:9.7 occ:0.77 OE2 B:GLU126 1.9 17.4 1.0 OE1 A:GLU53 2.0 13.5 1.0 OE2 A:GLU20 2.1 12.5 1.0 ND1 A:HIS56 2.2 11.3 1.0 OE1 A:GLU20 2.2 12.8 1.0 O A:HOH335 2.3 18.0 0.7 O A:HOH335 2.3 9.2 0.3 CD A:GLU20 2.5 11.0 1.0 CD B:GLU126 2.9 12.6 1.0 CD A:GLU53 3.1 12.4 1.0 CE1 A:HIS56 3.1 12.0 1.0 OE1 B:GLU126 3.1 15.0 1.0 CG A:HIS56 3.3 10.1 1.0 OE2 A:GLU53 3.7 15.3 1.0 FE B:FE201 3.7 12.3 0.7 CB A:HIS56 3.7 9.5 1.0 O B:HOH311 3.9 20.0 0.5 CG A:GLU20 4.0 11.1 1.0 O B:HOH304 4.2 29.6 1.0 CG A:GLU53 4.2 11.1 1.0 CA A:GLU53 4.2 9.6 1.0 CG B:GLU126 4.3 11.6 1.0 NE2 A:HIS56 4.3 10.5 1.0 OE1 B:GLU95 4.3 20.3 1.0 CD2 A:HIS56 4.4 9.4 1.0 CB A:GLU53 4.4 10.0 1.0 OH B:TYR100 4.7 12.6 1.0 CE1 B:HIS129 4.7 12.4 1.0 CE1 B:TYR100 4.8 12.4 1.0 CB A:GLU20 4.8 10.3 1.0 N A:GLU53 4.8 9.0 1.0 O A:GLY52 4.9 10.2 1.0 ND1 B:HIS129 4.9 12.1 1.0

Iron binding site 2 out of 4 in the Dife-Sulerythrin Oxidised By H2O2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dife-Sulerythrin Oxidised By H2O2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:10.4 occ:0.69 OE2 A:GLU126 2.0 13.5 1.0 OE1 B:GLU53 2.0 12.7 1.0 ND1 A:HIS129 2.1 9.2 1.0 OE1 A:GLU92 2.1 14.6 1.0 O A:HOH321 2.3 16.4 0.6 OE2 A:GLU92 2.3 13.5 1.0 CD A:GLU92 2.5 12.5 1.0 O B:HOH306 2.8 12.3 0.5 CD B:GLU53 2.9 11.2 1.0 CE1 A:HIS129 3.1 10.2 1.0 CD A:GLU126 3.1 10.8 1.0 OE2 B:GLU53 3.2 10.9 1.0 CG A:HIS129 3.2 8.7 1.0 CB A:HIS129 3.6 9.0 1.0 OE1 A:GLU126 3.7 15.6 1.0 O B:HOH306 3.7 14.8 0.5 FE B:FE202 3.8 9.4 0.9 CG A:GLU92 4.0 11.8 1.0 CG A:GLU126 4.1 9.9 1.0 NE2 A:HIS129 4.2 9.2 1.0 OE1 A:GLU95 4.2 18.9 1.0 CA A:GLU126 4.2 8.8 1.0 CG B:GLU53 4.3 8.6 1.0 CD2 A:HIS129 4.3 8.6 1.0 OH B:TYR27 4.4 12.0 1.0 CB A:GLU126 4.4 9.4 1.0 CE1 B:TYR27 4.5 9.6 1.0 CG2 B:ILE49 4.5 8.7 1.0 CB A:GLU92 4.9 10.8 1.0 CZ B:TYR27 4.9 9.9 1.0

Iron binding site 3 out of 4 in the Dife-Sulerythrin Oxidised By H2O2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dife-Sulerythrin Oxidised By H2O2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:12.3 occ:0.68 OE1 B:GLU126 1.9 15.0 1.0 OE2 A:GLU53 2.0 15.3 1.0 OE2 B:GLU92 2.2 16.1 1.0 ND1 B:HIS129 2.2 12.1 1.0 O B:HOH311 2.2 20.0 0.5 OE1 B:GLU92 2.3 15.2 1.0 CD B:GLU92 2.5 14.8 1.0 O A:HOH335 2.6 9.2 0.3 CD A:GLU53 2.9 12.4 1.0 CE1 B:HIS129 3.0 12.4 1.0 CD B:GLU126 3.1 12.6 1.0 OE1 A:GLU53 3.1 13.5 1.0 CG B:HIS129 3.3 11.4 1.0 O A:HOH335 3.6 18.0 0.7 CB B:HIS129 3.7 11.9 1.0 OE2 B:GLU126 3.7 17.4 1.0 FE A:FE201 3.7 9.7 0.8 CG B:GLU92 4.0 14.6 1.0 CG B:GLU126 4.1 11.6 1.0 OE1 B:GLU95 4.2 20.3 1.0 CA B:GLU126 4.2 10.8 1.0 NE2 B:HIS129 4.3 12.2 1.0 CG A:GLU53 4.3 11.1 1.0 CB B:GLU126 4.4 10.9 1.0 CD2 B:HIS129 4.4 12.7 1.0 OH A:TYR27 4.4 13.4 1.0 CG2 A:ILE49 4.5 10.7 1.0 CE1 A:TYR27 4.6 11.1 1.0 CB B:GLU92 4.9 12.3 1.0 CZ A:TYR27 5.0 11.2 1.0

Iron binding site 4 out of 4 in the Dife-Sulerythrin Oxidised By H2O2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dife-Sulerythrin Oxidised By H2O2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:9.4 occ:0.89 OE1 A:GLU126 2.0 15.6 1.0 OE2 B:GLU53 2.0 10.9 1.0 OE1 B:GLU20 2.1 10.6 1.0 OE2 B:GLU20 2.2 11.4 1.0 ND1 B:HIS56 2.2 9.3 1.0 O B:HOH306 2.2 14.8 0.5 O B:HOH306 2.3 12.3 0.5 CD B:GLU20 2.5 9.8 1.0 CD A:GLU126 2.9 10.8 1.0 CD B:GLU53 3.1 11.2 1.0 CE1 B:HIS56 3.1 9.7 1.0 OE2 A:GLU126 3.1 13.5 1.0 CG B:HIS56 3.3 8.0 1.0 OE1 B:GLU53 3.7 12.7 1.0 CB B:HIS56 3.7 7.6 1.0 FE A:FE202 3.8 10.4 0.7 O A:HOH321 3.9 16.4 0.6 CG B:GLU20 4.0 10.5 1.0 CG B:GLU53 4.2 8.6 1.0 CA B:GLU53 4.2 7.7 1.0 O A:HOH329 4.3 25.8 1.0 CG A:GLU126 4.3 9.9 1.0 NE2 B:HIS56 4.3 7.6 1.0 CD2 B:HIS56 4.4 7.4 1.0 OE1 A:GLU95 4.4 18.9 1.0 CB B:GLU53 4.4 8.5 1.0 CE1 A:HIS129 4.7 10.2 1.0 OH A:TYR100 4.7 10.7 1.0 CE1 A:TYR100 4.8 10.2 1.0 ND1 A:HIS129 4.8 9.2 1.0 CB B:GLU20 4.8 9.4 1.0 N B:GLU53 4.9 8.0 1.0 O B:GLY52 4.9 8.8 1.0

J.H.Jeoung, S.Runger, M.Haumann, B.Neumann, F.Klemke, V.Davis, A.Fischer, H.Dau, U.Wollenberger, H.Dobbek. Bimetallic Mn, Fe, Co, and Ni Sites in A Four-Helix Bundle Protein: Metal Binding, Structure, and Peroxide Activation. Inorg.Chem. 2021.
ISSN: ISSN 0020-1669
PubMed: 34757735
DOI: 10.1021/ACS.INORGCHEM.1C01919