Iron in PDB 7o8a: Dife-Sulerythrin Reduced with Na-Dithionite

The structure of Dife-Sulerythrin Reduced with Na-Dithionite, PDB code: 7o8a 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)	46.12 / 1.21
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	101.762, 88.38, 60.361, 90, 114.97, 90
R / Rfree (%)	14.7 / 18.3

The structure of Dife-Sulerythrin Reduced with Na-Dithionite also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Iron atom in the Dife-Sulerythrin Reduced with Na-Dithionite (pdb code 7o8a). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Dife-Sulerythrin Reduced with Na-Dithionite, PDB code: 7o8a:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe202 b:13.6 occ:1.00 OE1 A:GLU53 2.0 13.4 1.0 O A:HOH323 2.2 21.1 1.0 ND1 A:HIS56 2.2 12.0 1.0 OE2 A:GLU20 2.2 14.1 1.0 OE1 A:GLU20 2.3 14.2 1.0 CD A:GLU20 2.6 13.9 1.0 CD A:GLU53 3.1 12.5 1.0 CE1 A:HIS56 3.1 13.2 1.0 CG A:HIS56 3.3 11.7 1.0 CB A:HIS56 3.7 12.8 1.0 OE2 A:GLU53 3.8 13.3 1.0 CG A:GLU20 4.1 13.4 1.0 CA A:GLU53 4.2 11.4 1.0 CG A:GLU53 4.2 12.3 1.0 CB A:GLU53 4.3 12.2 1.0 NE2 A:HIS56 4.3 13.3 1.0 CD2 A:HIS56 4.4 12.5 1.0 N A:GLU53 4.9 11.5 1.0 CB A:GLU20 4.9 12.0 1.0 O A:GLY52 5.0 13.6 1.0

Iron binding site 2 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe203 b:13.7 occ:1.00 OE2 A:GLU126 2.0 14.1 1.0 ND1 A:HIS129 2.2 11.9 1.0 OE2 A:GLU92 2.2 13.3 1.0 O A:HOH329 2.2 20.1 1.0 OE1 A:GLU92 2.3 16.2 1.0 CD A:GLU92 2.6 15.0 1.0 CE1 A:HIS129 3.1 14.3 1.0 CD A:GLU126 3.1 13.9 1.0 CG A:HIS129 3.3 12.8 1.0 CB A:HIS129 3.7 14.0 1.0 OE1 A:GLU126 3.8 14.3 1.0 CG A:GLU92 4.1 12.8 1.0 OE1 A:GLU95 4.1 22.7 1.0 CG A:GLU126 4.1 13.0 1.0 CA A:GLU126 4.2 14.4 1.0 CB A:GLU126 4.2 13.7 1.0 NE2 A:HIS129 4.3 13.8 1.0 CD2 A:HIS129 4.4 12.4 1.0 CB A:GLU92 4.9 11.8 1.0 N A:GLU126 5.0 13.1 1.0

Iron binding site 3 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:13.6 occ:0.91 OE2 B:GLU126 2.0 15.4 1.0 OE2 C:GLU53 2.1 13.9 1.0 OE2 B:GLU92 2.2 15.5 1.0 ND1 B:HIS129 2.2 13.1 1.0 OE1 B:GLU92 2.2 16.1 1.0 O B:HOH304 2.3 22.7 1.0 CD B:GLU92 2.5 16.2 1.0 CD C:GLU53 3.0 13.5 1.0 CD B:GLU126 3.1 14.5 1.0 CE1 B:HIS129 3.1 14.8 1.0 OE1 C:GLU53 3.2 13.9 1.0 CG B:HIS129 3.3 14.4 1.0 O C:HOH376 3.6 26.1 1.0 CB B:HIS129 3.7 13.9 1.0 OE1 B:GLU126 3.8 16.2 1.0 FE C:FE202 3.9 12.9 0.9 CG B:GLU92 4.0 15.6 1.0 OE1 B:GLU95 4.1 24.7 1.0 CG B:GLU126 4.1 14.6 1.0 CA B:GLU126 4.2 13.5 1.0 CB B:GLU126 4.3 13.9 1.0 NE2 B:HIS129 4.3 14.2 1.0 CG C:GLU53 4.4 13.4 1.0 CD2 B:HIS129 4.4 14.4 1.0 CG2 C:ILE49 4.4 13.3 1.0 OH C:TYR27 4.5 16.0 1.0 CE1 C:TYR27 4.6 13.8 1.0 CB B:GLU92 4.9 14.0 1.0 N B:GLU126 5.0 13.2 1.0

Iron binding site 4 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe203 b:12.7 occ:0.96 OE1 C:GLU126 2.1 15.0 1.0 OE1 B:GLU53 2.1 13.0 1.0 O B:HOH315 2.2 14.6 0.5 ND1 B:HIS56 2.2 12.9 1.0 OE2 B:GLU20 2.2 13.7 1.0 OE1 B:GLU20 2.3 14.7 1.0 O B:HOH315 2.3 26.9 0.5 CD B:GLU20 2.6 13.7 1.0 CD C:GLU126 2.9 13.1 1.0 OE2 C:GLU126 3.1 14.1 1.0 CE1 B:HIS56 3.1 12.2 1.0 CD B:GLU53 3.1 11.8 1.0 CG B:HIS56 3.3 12.4 1.0 CB B:HIS56 3.7 12.2 1.0 OE2 B:GLU53 3.7 13.4 1.0 FE C:FE201 3.9 12.6 0.9 O C:HOH318 4.0 19.1 1.0 CG B:GLU20 4.1 13.6 1.0 CA B:GLU53 4.2 11.3 1.0 CG B:GLU53 4.2 12.1 1.0 CG C:GLU126 4.3 13.9 1.0 NE2 B:HIS56 4.3 12.9 1.0 CB B:GLU53 4.4 12.3 1.0 O C:HOH309 4.4 34.9 1.0 CD2 B:HIS56 4.4 12.2 1.0 OE1 C:GLU95 4.6 25.9 1.0 OH C:TYR100 4.7 14.1 1.0 CE1 C:TYR100 4.8 13.2 1.0 CE1 C:HIS129 4.8 12.0 1.0 N B:GLU53 4.9 12.4 1.0 CB B:GLU20 4.9 12.8 1.0 ND1 C:HIS129 5.0 12.7 1.0

Iron binding site 5 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:12.6 occ:0.95 OE2 C:GLU126 2.0 14.1 1.0 OE2 B:GLU53 2.1 13.4 1.0 ND1 C:HIS129 2.2 12.7 1.0 OE1 C:GLU92 2.2 14.7 1.0 OE2 C:GLU92 2.2 13.0 1.0 O C:HOH318 2.2 19.1 1.0 CD C:GLU92 2.5 11.8 1.0 O B:HOH315 3.0 26.9 0.5 CD B:GLU53 3.0 11.8 1.0 CD C:GLU126 3.1 13.1 1.0 CE1 C:HIS129 3.1 12.0 1.0 OE1 B:GLU53 3.2 13.0 1.0 CG C:HIS129 3.3 12.3 1.0 CB C:HIS129 3.7 12.9 1.0 OE1 C:GLU126 3.8 15.0 1.0 O B:HOH315 3.9 14.6 0.5 FE B:FE203 3.9 12.7 1.0 CG C:GLU92 4.0 15.0 1.0 CG C:GLU126 4.1 13.9 1.0 OE1 C:GLU95 4.2 25.9 1.0 CA C:GLU126 4.3 12.3 1.0 CB C:GLU126 4.3 12.9 1.0 NE2 C:HIS129 4.3 12.6 1.0 CG B:GLU53 4.4 12.1 1.0 CD2 C:HIS129 4.4 11.9 1.0 OH B:TYR27 4.5 13.9 1.0 CG2 B:ILE49 4.5 13.2 1.0 CE1 B:TYR27 4.6 13.0 1.0 CB C:GLU92 4.9 13.9 1.0

Iron binding site 6 out of 6 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe202 b:12.9 occ:0.90 OE1 C:GLU53 2.0 13.9 1.0 OE1 B:GLU126 2.0 16.2 1.0 ND1 C:HIS56 2.2 12.9 1.0 O C:HOH376 2.2 26.1 1.0 OE2 C:GLU20 2.2 14.3 1.0 OE1 C:GLU20 2.3 14.8 1.0 CD C:GLU20 2.6 14.1 1.0 CD B:GLU126 2.9 14.5 1.0 CE1 C:HIS56 3.1 15.2 1.0 OE2 B:GLU126 3.1 15.4 1.0 CD C:GLU53 3.1 13.5 1.0 CG C:HIS56 3.3 11.5 1.0 CB C:HIS56 3.7 12.7 1.0 OE2 C:GLU53 3.8 13.9 1.0 FE B:FE201 3.9 13.6 0.9 O B:HOH304 4.0 22.7 1.0 CG C:GLU20 4.1 14.9 1.0 CA C:GLU53 4.2 12.8 1.0 CG C:GLU53 4.2 13.4 1.0 NE2 C:HIS56 4.3 13.6 1.0 CG B:GLU126 4.3 14.6 1.0 CB C:GLU53 4.3 12.9 1.0 CD2 C:HIS56 4.4 12.4 1.0 OE1 B:GLU95 4.6 24.7 1.0 OH B:TYR100 4.7 16.3 1.0 CE1 B:TYR100 4.8 14.2 1.0 N C:GLU53 4.9 12.4 1.0 CB C:GLU20 4.9 12.3 1.0 OE2 B:GLU95 5.0 35.9 1.0 O C:GLY52 5.0 13.6 1.0 CE1 B:HIS129 5.0 14.8 1.0 CD B:GLU95 5.0 21.6 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