Cobalt in PDB 7o99: Dimn-Sulerythrin

The structure of Dimn-Sulerythrin, PDB code: 7o99 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)	38.78 / 1.24
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	72.756, 72.756, 98.41, 90, 90, 120
R / Rfree (%)	12.2 / 15.6

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

Chlorine

(Cl)

1 atom

The binding sites of Cobalt atom in the Dimn-Sulerythrin (pdb code 7o99). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 5 binding sites of Cobalt where determined in the Dimn-Sulerythrin, PDB code: 7o99:
Jump to Cobalt binding site number: 1; 2; 3; 4; 5;

Cobalt binding site 1 out of 5 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co201 b:11.3 occ:0.93 OE2 A:GLU126 1.9 20.4 1.0 OE2 B:GLU53 2.0 11.5 1.0 ND1 A:HIS129 2.1 10.0 1.0 OE1 A:GLU92 2.1 14.6 1.0 OE2 A:GLU92 2.3 17.7 1.0 O B:HOH366 2.3 27.9 1.0 CD A:GLU92 2.5 16.5 1.0 CD B:GLU53 2.9 10.1 1.0 CE1 A:HIS129 3.0 10.6 1.0 CD A:GLU126 3.0 12.4 1.0 OE1 B:GLU53 3.2 12.3 1.0 CG A:HIS129 3.2 10.1 1.0 O A:HOH381 3.5 21.2 1.0 CB A:HIS129 3.5 10.5 1.0 OE1 A:GLU126 3.7 18.3 1.0 CO B:CO202 3.8 10.8 0.9 CG A:GLU92 4.0 18.6 1.0 CG A:GLU126 4.2 11.0 1.0 NE2 A:HIS129 4.2 10.6 1.0 CA A:GLU126 4.3 11.2 1.0 CD2 A:HIS129 4.3 10.1 1.0 CG B:GLU53 4.3 9.5 1.0 OE1 A:GLU95 4.3 26.6 1.0 CG2 B:ILE49 4.3 10.6 1.0 OH B:TYR27 4.4 16.9 1.0 CB A:GLU126 4.4 10.9 1.0 CE2 B:TYR27 4.5 11.4 1.0 CB A:GLU92 4.8 14.2 1.0 CZ B:TYR27 4.9 12.4 1.0

Cobalt binding site 2 out of 5 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co202 b:14.9 occ:0.95 OE1 B:GLU126 1.9 21.1 1.0 OE1 A:GLU53 2.0 15.8 1.0 OE2 A:GLU20 2.1 17.0 1.0 ND1 A:HIS56 2.2 13.9 1.0 O B:HOH385 2.2 22.6 1.0 OE1 A:GLU20 2.2 17.9 1.0 CD A:GLU20 2.5 15.6 1.0 CD B:GLU126 2.9 16.1 1.0 CD A:GLU53 3.0 13.3 1.0 CE1 A:HIS56 3.0 14.5 1.0 OE2 B:GLU126 3.1 22.2 1.0 CG A:HIS56 3.2 13.7 1.0 CB A:HIS56 3.6 13.4 1.0 OE2 A:GLU53 3.7 14.9 1.0 CO B:CO201 3.9 16.7 1.0 O B:HOH352 4.0 29.5 1.0 CG A:GLU20 4.0 14.9 1.0 CA A:GLU53 4.1 11.8 1.0 CG A:GLU53 4.1 13.3 1.0 NE2 A:HIS56 4.2 13.6 1.0 O B:HOH304 4.3 41.5 1.0 CG B:GLU126 4.3 15.8 1.0 CB A:GLU53 4.3 13.4 1.0 CD2 A:HIS56 4.3 14.2 1.0 OE1 B:GLU95 4.5 29.5 1.0 OH B:TYR100 4.7 17.3 1.0 N A:GLU53 4.8 12.5 1.0 CE2 B:TYR100 4.8 15.6 1.0 CE1 B:HIS129 4.8 14.6 1.0 CB A:GLU20 4.8 13.6 1.0 O A:GLY52 4.9 13.3 1.0 ND1 B:HIS129 5.0 14.3 1.0

Cobalt binding site 3 out of 5 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co201 b:16.7 occ:0.97 OE2 A:GLU53 2.0 14.9 1.0 OE2 B:GLU126 2.0 22.2 1.0 ND1 B:HIS129 2.1 14.3 1.0 OE2 B:GLU92 2.2 23.7 1.0 OE1 B:GLU92 2.2 18.7 1.0 O B:HOH352 2.3 29.5 1.0 CD B:GLU92 2.5 20.2 1.0 CD A:GLU53 2.9 13.3 1.0 CE1 B:HIS129 3.0 14.6 1.0 CD B:GLU126 3.1 16.1 1.0 OE1 A:GLU53 3.2 15.8 1.0 CG B:HIS129 3.2 15.7 1.0 CB B:HIS129 3.5 15.9 1.0 O B:HOH385 3.6 22.6 1.0 OE1 B:GLU126 3.7 21.1 1.0 CO A:CO202 3.9 14.9 0.9 CG B:GLU92 4.0 23.0 1.0 CG B:GLU126 4.1 15.8 1.0 NE2 B:HIS129 4.2 14.5 1.0 CA B:GLU126 4.2 16.9 1.0 CD2 B:HIS129 4.3 14.5 1.0 CG A:GLU53 4.3 13.3 1.0 OE1 B:GLU95 4.3 29.5 1.0 OH A:TYR27 4.3 19.0 1.0 CG2 A:ILE49 4.3 14.7 1.0 CB B:GLU126 4.3 16.3 1.0 CE2 A:TYR27 4.5 15.1 1.0 CB B:GLU92 4.8 20.5 1.0 CZ A:TYR27 4.9 15.1 1.0

Cobalt binding site 4 out of 5 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co202 b:10.8 occ:0.90 OE1 A:GLU126 2.0 18.3 1.0 OE1 B:GLU53 2.0 12.3 1.0 OE2 B:GLU20 2.1 13.2 1.0 ND1 B:HIS56 2.1 10.4 1.0 O A:HOH381 2.2 21.2 1.0 OE1 B:GLU20 2.3 14.5 1.0 CD B:GLU20 2.5 11.9 1.0 CD A:GLU126 2.9 12.4 1.0 CE1 B:HIS56 3.0 10.8 1.0 CD B:GLU53 3.1 10.1 1.0 OE2 A:GLU126 3.2 20.4 1.0 CG B:HIS56 3.2 9.9 1.0 OE2 B:GLU53 3.6 11.5 1.0 CB B:HIS56 3.6 9.9 1.0 CO A:CO201 3.8 11.3 0.9 O B:HOH366 3.9 27.9 1.0 CG B:GLU20 4.0 12.7 1.0 CA B:GLU53 4.1 9.8 1.0 CG B:GLU53 4.2 9.5 1.0 NE2 B:HIS56 4.2 10.0 1.0 CG A:GLU126 4.2 11.0 1.0 CB B:GLU53 4.3 9.6 1.0 CD2 B:HIS56 4.3 9.8 1.0 O A:HOH314 4.3 42.0 1.0 OE1 A:GLU95 4.4 26.6 1.0 OH A:TYR100 4.7 13.3 1.0 CE1 A:HIS129 4.8 10.6 1.0 N B:GLU53 4.8 9.5 1.0 CE2 A:TYR100 4.8 12.1 1.0 CB B:GLU20 4.9 11.6 1.0 ND1 A:HIS129 4.9 10.0 1.0 O B:GLY52 4.9 10.1 1.0

Cobalt binding site 5 out of 5 in the Dimn-Sulerythrin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 5 of Dimn-Sulerythrin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:18.1 occ:0.80 ND1 B:HIS0 2.1 22.2 1.0 N B:GLY-1 2.1 23.3 1.0 N B:HIS0 2.1 20.0 1.0 O B:HOH416 2.2 26.1 1.0 C B:GLY-1 2.9 20.4 1.0 CA B:GLY-1 3.0 21.9 1.0 CG B:HIS0 3.1 20.6 1.0 CE1 B:HIS0 3.1 22.3 1.0 CA B:HIS0 3.2 20.1 1.0 CB B:HIS0 3.4 20.7 1.0 N B:MET1 3.8 19.3 1.0 C B:HIS0 4.0 21.6 1.0 O B:HOH450 4.1 31.9 1.0 O B:GLY-1 4.2 21.3 1.0 CD2 B:HIS0 4.2 22.9 1.0 NE2 B:HIS0 4.2 24.6 1.0 O B:HOH457 4.3 48.9 1.0 O B:HOH477 4.4 29.0 1.0 O A:HOH307 4.4 29.7 1.0 CG B:MET1 4.9 22.7 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