Manganese in PDB 7o93: Dimn-Sulerythrin

The structure of Dimn-Sulerythrin, PDB code: 7o93 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 / 1.17
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.611, 72.611, 99.272, 90, 90, 120
R / Rfree (%)	12.5 / 14.4

The structure of Dimn-Sulerythrin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Manganese atom in the Dimn-Sulerythrin (pdb code 7o93). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Dimn-Sulerythrin, PDB code: 7o93:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn202 b:9.1 occ:0.89 OE2 B:GLU53 2.1 9.6 1.0 OE2 A:GLU126 2.1 9.9 1.0 ND1 A:HIS129 2.2 9.2 1.0 OE2 A:GLU92 2.2 10.5 1.0 O1 A:PEO204 2.2 12.6 0.8 OE1 A:GLU92 2.3 10.8 1.0 CD A:GLU92 2.6 10.2 1.0 CD B:GLU53 3.0 9.0 1.0 CE1 A:HIS129 3.1 9.7 1.0 CD A:GLU126 3.1 9.2 1.0 O2 A:PEO204 3.2 11.9 0.8 OE1 B:GLU53 3.2 9.4 1.0 CG A:HIS129 3.3 8.9 1.0 CB A:HIS129 3.7 9.3 1.0 MN B:MN201 3.8 8.6 0.9 OE1 A:GLU126 3.8 11.2 1.0 OE1 A:GLU95 4.1 16.4 1.0 CG A:GLU92 4.1 10.6 1.0 CG A:GLU126 4.1 9.8 1.0 CA A:GLU126 4.2 9.2 1.0 CB A:GLU126 4.3 9.0 1.0 NE2 A:HIS129 4.3 9.8 1.0 CG B:GLU53 4.4 8.5 1.0 CD2 A:HIS129 4.4 9.4 1.0 CG2 B:ILE49 4.4 9.1 1.0 OH B:TYR27 4.5 11.4 1.0 CE2 B:TYR27 4.5 9.6 1.0 O A:HOH407 4.7 18.9 1.0 CB A:GLU92 4.9 10.5 1.0

Manganese binding site 2 out of 4 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mn203 b:12.2 occ:0.94 OE1 B:GLU126 2.1 14.6 1.0 OE1 A:GLU53 2.1 12.4 1.0 OE2 A:GLU20 2.2 12.9 1.0 ND1 A:HIS56 2.2 13.1 1.0 O1 B:PEO203 2.3 14.6 0.8 OE1 A:GLU20 2.3 13.3 1.0 CD A:GLU20 2.6 12.2 1.0 CD B:GLU126 2.9 13.9 1.0 OE2 B:GLU126 3.1 14.4 1.0 CD A:GLU53 3.1 12.0 1.0 CE1 A:HIS56 3.1 13.1 1.0 O2 B:PEO203 3.3 15.9 0.8 CG A:HIS56 3.3 12.6 1.0 CB A:HIS56 3.7 12.0 1.0 OE2 A:GLU53 3.7 13.3 1.0 MN B:MN202 3.8 13.1 0.9 CG A:GLU20 4.1 11.7 1.0 CA A:GLU53 4.2 11.4 1.0 CG A:GLU53 4.2 11.1 1.0 O B:HOH302 4.3 24.1 1.0 CG B:GLU126 4.3 14.1 1.0 NE2 A:HIS56 4.3 13.3 1.0 CB A:GLU53 4.3 10.7 1.0 OE1 B:GLU95 4.4 19.2 0.5 OE2 B:GLU95 4.4 21.4 0.5 CD2 A:HIS56 4.4 12.8 1.0 OE1 B:GLU95 4.5 19.2 0.5 OH B:TYR100 4.7 14.4 1.0 CD B:GLU95 4.7 17.9 0.5 CE2 B:TYR100 4.8 13.8 1.0 CE1 B:HIS129 4.8 13.3 1.0 N A:GLU53 4.9 11.0 1.0 CB A:GLU20 4.9 11.2 1.0 O A:GLY52 4.9 12.2 1.0 ND1 B:HIS129 5.0 13.4 1.0

Manganese binding site 3 out of 4 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn201 b:8.6 occ:0.87 OE1 A:GLU126 2.1 11.2 1.0 OE1 B:GLU53 2.1 9.4 1.0 OE2 B:GLU20 2.2 10.1 1.0 ND1 B:HIS56 2.2 8.8 1.0 O2 A:PEO204 2.2 11.9 0.8 OE1 B:GLU20 2.3 10.5 1.0 CD B:GLU20 2.6 9.5 1.0 CD A:GLU126 2.9 9.2 1.0 OE2 A:GLU126 3.1 9.9 1.0 CE1 B:HIS56 3.1 9.5 1.0 CD B:GLU53 3.1 9.0 1.0 CG B:HIS56 3.3 8.8 1.0 O1 A:PEO204 3.3 12.6 0.8 CB B:HIS56 3.7 9.2 1.0 OE2 B:GLU53 3.8 9.6 1.0 MN A:MN202 3.8 9.1 0.9 CG B:GLU20 4.1 9.9 1.0 CA B:GLU53 4.2 8.3 1.0 CG B:GLU53 4.2 8.5 1.0 O A:HOH329 4.3 19.5 1.0 CG A:GLU126 4.3 9.8 1.0 NE2 B:HIS56 4.3 9.7 1.0 CB B:GLU53 4.3 8.4 1.0 CD2 B:HIS56 4.4 9.4 1.0 OE1 A:GLU95 4.6 16.4 1.0 OH A:TYR100 4.7 11.0 1.0 CE2 A:TYR100 4.8 10.2 1.0 CE1 A:HIS129 4.8 9.7 1.0 N B:GLU53 4.9 8.3 1.0 CB B:GLU20 4.9 9.8 1.0 O B:GLY52 5.0 9.3 1.0 ND1 A:HIS129 5.0 9.2 1.0

Manganese binding site 4 out of 4 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mn202 b:13.1 occ:0.92 OE2 A:GLU53 2.1 13.3 1.0 OE2 B:GLU126 2.1 14.4 1.0 ND1 B:HIS129 2.2 13.4 1.0 OE2 B:GLU92 2.2 14.4 1.0 O2 B:PEO203 2.2 15.9 0.8 OE1 B:GLU92 2.3 13.9 1.0 CD B:GLU92 2.6 13.5 1.0 CD A:GLU53 3.0 12.0 1.0 CE1 B:HIS129 3.1 13.3 1.0 CD B:GLU126 3.1 13.9 1.0 OE1 A:GLU53 3.2 12.4 1.0 O1 B:PEO203 3.2 14.6 0.8 CG B:HIS129 3.3 13.7 1.0 CB B:HIS129 3.7 14.0 1.0 MN A:MN203 3.8 12.2 0.9 OE1 B:GLU126 3.8 14.6 1.0 OE1 B:GLU95 3.8 19.2 0.5 CG B:GLU92 4.1 14.3 1.0 CG B:GLU126 4.2 14.1 1.0 CA B:GLU126 4.2 15.0 1.0 OE1 B:GLU95 4.2 19.2 0.5 NE2 B:HIS129 4.3 13.8 1.0 CB B:GLU126 4.3 14.4 1.0 CG A:GLU53 4.4 11.1 1.0 CD2 B:HIS129 4.4 14.0 1.0 CG2 A:ILE49 4.4 12.3 1.0 OH A:TYR27 4.5 15.1 1.0 CE2 A:TYR27 4.6 12.8 1.0 CD B:GLU95 4.9 17.9 0.5 O B:HOH389 4.9 27.3 1.0 CB B:GLU92 4.9 14.8 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