Cobalt in PDB 7dgn: The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin

The structure of The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgn was solved by S.Nagao, A.Idomoto, N.Shibata, Y.Higuchi, S.Hirota, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.01 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.966, 63.463, 83.003, 90, 90, 90
R / Rfree (%)	20.2 / 26.9

The structure of The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Cobalt atom in the The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin (pdb code 7dgn). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgn:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co203 b:55.2 occ:1.00 O B:HOH328 1.9 31.7 1.0 OD2 A:ASP141 2.0 48.7 1.0 NE2 A:HIS82 2.1 52.7 1.0 ND1 B:HIS79 2.1 49.5 1.0 CE1 A:HIS82 2.9 54.9 1.0 CE1 B:HIS79 3.0 49.5 1.0 CG B:HIS79 3.2 39.0 1.0 CG A:ASP141 3.3 43.0 1.0 CD2 A:HIS82 3.3 52.5 1.0 CB B:HIS79 3.6 37.4 1.0 O B:HOH327 3.7 54.0 1.0 CG2 B:ILE75 4.0 50.7 1.0 CB A:ASP141 4.0 39.9 1.0 ND1 A:HIS82 4.1 49.1 1.0 O A:HOH330 4.2 39.4 1.0 OD1 A:ASP141 4.2 43.2 1.0 NE2 B:HIS79 4.2 43.5 1.0 CG A:HIS82 4.3 49.8 1.0 CD2 B:HIS79 4.3 39.4 1.0 O B:ILE75 4.5 41.9 1.0 CA A:PHE138 4.6 35.7 1.0 CA B:HIS79 4.6 37.3 1.0 O A:LEU137 4.7 33.6 1.0 N A:PHE138 4.9 35.7 1.0 C A:LEU137 4.9 41.2 1.0

Cobalt binding site 2 out of 2 in the The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:51.4 occ:1.00 O A:HOH334 1.9 30.8 1.0 OD2 B:ASP141 2.0 56.0 1.0 NE2 B:HIS82 2.1 43.7 1.0 ND1 A:HIS79 2.1 43.5 1.0 CE1 B:HIS82 2.6 43.8 1.0 CE1 A:HIS79 3.0 42.7 1.0 CG B:ASP141 3.2 46.2 1.0 CG A:HIS79 3.2 41.2 1.0 CD2 B:HIS82 3.4 40.4 1.0 CB A:HIS79 3.6 34.2 1.0 ND1 B:HIS82 3.8 41.7 1.0 CB B:ASP141 3.9 39.9 1.0 OD1 B:ASP141 4.2 60.3 1.0 NE2 A:HIS79 4.2 40.5 1.0 CG B:HIS82 4.2 35.6 1.0 CD2 A:HIS79 4.3 40.3 1.0 CG2 A:ILE75 4.4 50.7 1.0 CA A:HIS79 4.5 34.9 1.0 O B:LEU137 4.6 38.1 1.0 O A:ILE75 4.7 44.4 1.0 CA B:PHE138 4.7 35.3 1.0 C B:LEU137 5.0 38.1 1.0

S.Nagao, A.Idomoto, N.Shibata, Y.Higuchi, S.Hirota. Rational Design of Metal-Binding Sites in Domain-Swapped Myoglobin Dimers. J.Inorg.Biochem. 2021.
ISSN: ISSN 0162-0134
DOI: 10.1016/J.JINORGBIO.2021.111374