Chlorine 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:

Iron

(Fe)

6 atoms

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

Chlorine binding site 1 out of 3 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl204 b:19.5 occ:1.00 N A:GLU41 3.2 14.1 1.0 O C:HOH429 3.2 34.2 1.0 O C:HOH301 3.3 39.5 1.0 CA A:TYR39 3.4 13.9 1.0 C A:TYR39 3.4 13.6 1.0 CB A:GLU41 3.5 19.0 1.0 N A:PRO40 3.6 13.0 1.0 N A:ILE42 3.6 13.2 1.0 CB A:TYR39 3.7 14.8 1.0 NZ C:LYS132 3.7 35.3 1.0 CE C:LYS132 3.7 25.8 1.0 CA A:GLU41 3.8 15.7 1.0 CD A:PRO40 3.8 14.4 1.0 CG A:GLU41 3.9 26.4 1.0 O A:TYR39 3.9 13.9 1.0 CD1 A:TYR39 4.0 19.8 1.0 CG1 A:ILE42 4.1 16.6 1.0 C A:GLU41 4.2 13.8 1.0 C A:PRO40 4.2 13.0 1.0 CG A:TYR39 4.3 15.0 1.0 CA A:PRO40 4.4 13.2 1.0 CG A:PRO40 4.5 14.9 1.0 CB A:ILE42 4.6 14.5 1.0 CD1 A:ILE42 4.7 17.8 1.0 N A:TYR39 4.7 14.1 1.0 CA A:ILE42 4.7 13.6 1.0 O A:GLY38 4.8 18.3 1.0 CD C:LYS132 5.0 23.9 1.0

Chlorine binding site 2 out of 3 in the Dife-Sulerythrin Reduced with Na-Dithionite


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl202 b:28.6 occ:1.00 OE2 B:GLU41 2.3 29.6 1.0 OE1 C:GLN139 2.9 25.5 1.0 N B:GLU41 3.3 14.3 1.0 CA B:TYR39 3.3 13.9 1.0 C B:TYR39 3.3 12.7 1.0 N B:ILE42 3.3 13.8 1.0 CB B:TYR39 3.4 14.1 1.0 CD B:GLU41 3.5 36.6 1.0 CB B:GLU41 3.5 15.7 1.0 O B:TYR39 3.6 13.8 1.0 N B:PRO40 3.7 13.7 1.0 CA B:GLU41 3.7 14.5 1.0 O C:HOH354 3.8 36.3 1.0 O B:HOH301 3.8 30.3 1.0 CG1 B:ILE42 3.8 16.0 1.0 CD1 B:TYR39 3.8 17.8 1.0 CG B:GLU41 4.0 25.0 1.0 C B:GLU41 4.0 13.6 1.0 CD C:GLN139 4.0 23.8 1.0 CG B:TYR39 4.1 14.7 1.0 CB B:ILE42 4.1 14.0 1.0 CD B:PRO40 4.2 14.1 1.0 CD1 B:ILE42 4.2 17.4 1.0 C B:PRO40 4.3 13.1 1.0 CA B:ILE42 4.3 13.6 1.0 NE2 C:GLN139 4.4 25.4 1.0 CA B:PRO40 4.5 14.0 1.0 OE1 B:GLU41 4.6 45.1 1.0 N B:TYR39 4.7 13.3 1.0 CG B:PRO40 4.9 14.4 1.0 O B:GLY38 5.0 17.4 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dife-Sulerythrin Reduced with Na-Dithionite within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:23.1 occ:1.00 N C:GLU41 3.2 15.0 0.7 N C:GLU41 3.2 14.8 0.3 CB C:GLU41 3.4 18.6 0.7 CA C:TYR39 3.4 15.0 1.0 C C:TYR39 3.4 14.3 1.0 CB C:GLU41 3.5 15.0 0.3 O B:HOH476 3.5 52.0 1.0 N C:PRO40 3.6 12.6 1.0 N C:ILE42 3.7 13.4 1.0 CB C:TYR39 3.7 15.6 1.0 CA C:GLU41 3.8 14.3 0.7 CA C:GLU41 3.8 13.7 0.3 NZ A:LYS132 3.8 43.9 1.0 CG C:GLU41 3.9 28.4 0.7 O C:TYR39 3.9 13.8 1.0 CD C:PRO40 3.9 15.7 1.0 CD1 C:TYR39 4.0 18.1 1.0 CE A:LYS132 4.1 40.5 1.0 CG1 C:ILE42 4.2 16.4 1.0 C C:PRO40 4.2 15.1 1.0 C C:GLU41 4.3 13.2 0.3 C C:GLU41 4.3 13.2 0.7 OE2 C:GLU41 4.3 54.1 0.7 CG C:TYR39 4.3 15.3 1.0 CA C:PRO40 4.4 12.6 1.0 CD C:GLU41 4.5 32.3 0.7 CG C:PRO40 4.5 15.6 1.0 CG C:GLU41 4.6 18.4 0.3 OE2 C:GLU41 4.6 26.4 0.3 CD1 C:ILE42 4.7 18.4 1.0 CB C:ILE42 4.7 14.6 1.0 N C:TYR39 4.7 13.9 1.0 O C:GLY38 4.8 17.9 1.0 CA C:ILE42 4.8 13.9 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