Cobalt in PDB 7o9d: Peroxide-Bound Dico-Sulerythrin

The structure of Peroxide-Bound Dico-Sulerythrin, PDB code: 7o9d 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)	38.86 / 1.28
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.539, 72.539, 98.912, 90, 90, 120
R / Rfree (%)	13.6 / 17.4

The structure of Peroxide-Bound Dico-Sulerythrin also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Cobalt atom in the Peroxide-Bound Dico-Sulerythrin (pdb code 7o9d). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 6 binding sites of Cobalt where determined in the Peroxide-Bound Dico-Sulerythrin, PDB code: 7o9d:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5; 6;

Cobalt binding site 1 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:14.0 occ:0.95 OE2 B:GLU126 1.9 15.8 1.0 OE1 A:GLU53 2.0 13.8 1.0 OE2 A:GLU20 2.1 14.3 1.0 ND1 A:HIS56 2.2 14.0 1.0 O1 B:PEO204 2.3 15.3 1.0 OE1 A:GLU20 2.3 15.2 1.0 CD A:GLU20 2.5 13.8 1.0 CD B:GLU126 2.9 15.1 1.0 CD A:GLU53 3.0 12.8 1.0 OE1 B:GLU126 3.1 16.4 1.0 CE1 A:HIS56 3.1 14.3 1.0 O2 B:PEO204 3.3 16.2 1.0 CG A:HIS56 3.3 14.0 1.0 OE2 A:GLU53 3.7 14.5 1.0 CB A:HIS56 3.7 14.4 1.0 CO B:CO201 3.7 14.6 0.9 CG A:GLU20 4.1 13.4 1.0 CG A:GLU53 4.1 12.5 1.0 CA A:GLU53 4.1 12.8 1.0 NE2 A:HIS56 4.3 14.7 1.0 O B:HOH301 4.3 24.0 1.0 CB A:GLU53 4.3 13.1 1.0 CG B:GLU126 4.3 15.6 1.0 OE2 B:GLU95 4.4 22.9 0.5 CD2 A:HIS56 4.4 14.1 1.0 OE1 B:GLU95 4.4 18.4 0.5 OE1 B:GLU95 4.6 19.6 0.5 OH B:TYR100 4.7 16.0 1.0 CE1 B:HIS129 4.7 13.9 1.0 CD B:GLU95 4.8 18.4 0.5 CE2 B:TYR100 4.8 15.3 1.0 N A:GLU53 4.8 12.5 1.0 CB A:GLU20 4.9 13.2 1.0 O A:GLY52 4.9 14.3 1.0 ND1 B:HIS129 4.9 14.7 1.0

Cobalt binding site 2 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:10.7 occ:0.95 OE2 A:GLU126 2.0 11.1 1.0 OE1 B:GLU53 2.0 10.6 1.0 ND1 A:HIS129 2.1 9.9 1.0 OE2 A:GLU92 2.2 12.1 1.0 OE1 A:GLU92 2.2 11.5 1.0 O1 A:PEO203 2.2 13.4 1.0 CD A:GLU92 2.5 11.6 1.0 CD B:GLU53 2.9 10.1 1.0 CE1 A:HIS129 3.0 11.4 1.0 CD A:GLU126 3.0 10.6 1.0 O2 A:PEO203 3.2 12.9 1.0 OE2 B:GLU53 3.2 10.1 1.0 CG A:HIS129 3.3 10.3 1.0 CB A:HIS129 3.6 10.3 1.0 OE1 A:GLU126 3.6 12.3 1.0 CO B:CO202 3.7 10.9 0.9 CG A:GLU126 4.0 10.0 1.0 CG A:GLU92 4.0 11.6 1.0 OE1 A:GLU95 4.1 17.4 1.0 CA A:GLU126 4.2 10.3 1.0 NE2 A:HIS129 4.2 10.4 1.0 CB A:GLU126 4.2 9.8 1.0 CG B:GLU53 4.3 9.2 1.0 CD2 A:HIS129 4.3 10.0 1.0 CG2 B:ILE49 4.4 10.5 1.0 OH B:TYR27 4.5 12.7 1.0 CE2 B:TYR27 4.6 10.8 1.0 O A:HOH356 4.7 20.6 1.0 CB A:GLU92 4.9 12.0 1.0

Cobalt binding site 3 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:14.6 occ:0.94 OE2 A:GLU53 2.0 14.5 1.0 OE1 B:GLU126 2.0 16.4 1.0 ND1 B:HIS129 2.1 14.7 1.0 OE1 B:GLU92 2.2 16.4 1.0 O2 B:PEO204 2.2 16.2 1.0 OE2 B:GLU92 2.2 15.2 1.0 CD B:GLU92 2.5 16.2 1.0 CD A:GLU53 2.9 12.8 1.0 CE1 B:HIS129 3.0 13.9 1.0 CD B:GLU126 3.0 15.1 1.0 O1 B:PEO204 3.1 15.3 1.0 OE1 A:GLU53 3.2 13.8 1.0 CG B:HIS129 3.3 15.6 1.0 OE2 B:GLU126 3.6 15.8 1.0 CB B:HIS129 3.7 14.9 1.0 CO A:CO201 3.7 14.0 0.9 OE1 B:GLU95 3.9 19.6 0.5 CG B:GLU92 4.0 16.8 1.0 CG B:GLU126 4.1 15.6 1.0 CA B:GLU126 4.1 16.6 1.0 NE2 B:HIS129 4.2 14.4 1.0 CB B:GLU126 4.2 15.6 1.0 OE1 B:GLU95 4.3 18.4 0.5 CG A:GLU53 4.3 12.5 1.0 CD2 B:HIS129 4.3 14.8 1.0 CG2 A:ILE49 4.4 13.6 1.0 OH A:TYR27 4.4 16.9 1.0 CE2 A:TYR27 4.6 14.4 1.0 CB B:GLU92 4.9 17.8 1.0 CD B:GLU95 4.9 18.4 0.5 N B:GLU126 5.0 15.9 1.0

Cobalt binding site 4 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:10.9 occ:0.95 OE1 A:GLU126 2.0 12.3 1.0 OE2 B:GLU53 2.0 10.1 1.0 OE1 B:GLU20 2.1 11.4 1.0 ND1 B:HIS56 2.2 10.0 1.0 O2 A:PEO203 2.2 12.9 1.0 OE2 B:GLU20 2.3 12.2 1.0 CD B:GLU20 2.5 11.4 1.0 CD A:GLU126 2.9 10.6 1.0 CD B:GLU53 3.0 10.1 1.0 CE1 B:HIS56 3.0 10.8 1.0 OE2 A:GLU126 3.1 11.1 1.0 CG B:HIS56 3.2 9.8 1.0 O1 A:PEO203 3.3 13.4 1.0 OE1 B:GLU53 3.7 10.6 1.0 CB B:HIS56 3.7 9.9 1.0 CO A:CO202 3.7 10.7 0.9 CG B:GLU20 4.0 11.4 1.0 CG B:GLU53 4.1 9.2 1.0 CA B:GLU53 4.1 10.0 1.0 O A:HOH310 4.2 20.1 1.0 CG A:GLU126 4.2 10.0 1.0 NE2 B:HIS56 4.3 10.3 1.0 CB B:GLU53 4.3 9.5 1.0 CD2 B:HIS56 4.4 10.0 1.0 OE1 A:GLU95 4.5 17.4 1.0 OH A:TYR100 4.7 12.2 1.0 CE1 A:HIS129 4.7 11.4 1.0 N B:GLU53 4.8 9.9 1.0 CE2 A:TYR100 4.8 11.0 1.0 CB B:GLU20 4.8 10.8 1.0 O B:GLY52 4.9 10.5 1.0 ND1 A:HIS129 4.9 9.9 1.0

Cobalt binding site 5 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:22.7 occ:0.50 CO B:CO203 0.0 22.7 0.5 CO B:CO203 1.7 28.7 0.5 O A:HOH304 2.0 31.8 1.0 N B:HIS0 2.0 40.5 1.0 ND1 B:HIS0 2.1 44.5 1.0 N B:GLY-1 2.7 47.3 1.0 C B:GLY-1 2.8 41.5 1.0 CA B:GLY-1 2.8 42.1 1.0 CG B:HIS0 3.0 43.2 1.0 CE1 B:HIS0 3.0 47.5 1.0 CA B:HIS0 3.1 40.5 1.0 CB B:HIS0 3.3 42.5 1.0 O B:HOH392 3.6 20.8 1.0 N B:MET1 3.8 27.8 1.0 OE2 A:GLU114 3.8 25.3 1.0 C B:HIS0 3.9 40.3 1.0 OE1 A:GLU114 4.0 29.2 1.0 O B:GLY-1 4.0 38.8 1.0 CD2 B:HIS0 4.1 46.0 1.0 NE2 B:HIS0 4.1 45.0 1.0 CD A:GLU114 4.3 26.4 1.0 CG B:MET1 4.8 51.6 1.0

Cobalt binding site 6 out of 6 in the Peroxide-Bound Dico-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 6 of Peroxide-Bound Dico-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:28.7 occ:0.50 CO B:CO203 0.0 28.7 0.5 CO B:CO203 1.7 22.7 0.5 N B:GLY-1 2.4 47.3 1.0 ND1 B:HIS0 2.6 44.5 1.0 CE1 B:HIS0 3.0 47.5 1.0 N B:HIS0 3.1 40.5 1.0 O B:HOH392 3.2 20.8 1.0 CA B:GLY-1 3.3 42.1 1.0 O A:HOH304 3.6 31.8 1.0 C B:GLY-1 3.6 41.5 1.0 N B:MET1 3.7 27.8 1.0 CG B:HIS0 3.8 43.2 1.0 CG B:MET1 3.9 51.6 1.0 CA B:HIS0 4.1 40.5 1.0 NE2 B:HIS0 4.2 45.0 1.0 C B:HIS0 4.3 40.3 1.0 CB B:MET1 4.4 37.6 1.0 CB B:HIS0 4.4 42.5 1.0 CD2 B:HIS0 4.6 46.0 1.0 CA B:MET1 4.7 28.9 1.0 O B:GLY-1 4.7 38.8 1.0 SD B:MET1 4.9 68.7 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