Cobalt in PDB 7dgk: The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin

The structure of The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin, PDB code: 7dgk 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)	33.08 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	55.202, 62.409, 82.553, 90, 90, 90
R / Rfree (%)	20.6 / 25.1

The structure of The Co-Bound Dimeric Structure of K78H/G80A/H82A 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 K78H/G80A/H82A Myoglobin (pdb code 7dgk). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 binding sites of Cobalt where determined in the The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin, PDB code: 7dgk:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 in the The Co-Bound Dimeric Structure of K78H/G80A/H82A 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 K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co203 b:33.2 occ:1.00 O B:HOH327 1.8 36.1 1.0 OE1 A:GLU85 1.9 35.0 1.0 NE2 B:HIS78 1.9 32.6 1.0 NE2 A:HIS81 2.0 33.5 1.0 CD2 B:HIS78 2.9 30.4 1.0 CE1 A:HIS81 3.0 36.9 1.0 CD A:GLU85 3.0 34.0 1.0 CD2 A:HIS81 3.0 33.1 1.0 CE1 B:HIS78 3.0 33.5 1.0 OE2 A:GLU85 3.4 32.8 1.0 O A:HOH334 3.8 46.1 1.0 CG B:HIS78 4.0 29.7 1.0 ND1 B:HIS78 4.1 29.7 1.0 ND1 A:HIS81 4.1 36.8 1.0 CG A:HIS81 4.1 34.2 1.0 O B:HOH361 4.2 32.7 1.0 CG A:GLU85 4.3 33.8 1.0 O A:HOH348 4.9 37.3 1.0 CB A:GLU85 5.0 34.3 1.0

Cobalt binding site 2 out of 4 in the The Co-Bound Dimeric Structure of K78H/G80A/H82A 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 K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Co204 b:39.4 occ:1.00 O A:HOH314 1.8 37.6 1.0 O A:HOH311 1.9 38.9 1.0 OD1 A:ASP122 1.9 44.0 1.0 CG A:ASP122 3.0 47.8 1.0 OD2 A:ASP122 3.4 47.9 1.0 ND2 B:ASN12 3.9 33.4 1.0 OD1 B:ASN12 4.0 34.6 1.0 CB A:ASP122 4.3 44.3 1.0 CG B:ASN12 4.4 30.9 1.0 NZ B:LYS16 4.5 42.3 1.0 CE B:LYS16 4.5 40.0 1.0 O A:GLY121 4.6 42.9 1.0 CA A:ASP122 5.0 45.5 1.0

Cobalt binding site 3 out of 4 in the The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 3 of The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co203 b:38.8 occ:1.00 O A:HOH305 1.7 33.0 1.0 OE2 B:GLU85 1.8 41.0 1.0 O B:HOH319 1.8 46.1 1.0 O B:HOH315 1.8 51.0 1.0 NE2 A:HIS78 1.9 31.9 1.0 NE2 B:HIS81 2.0 40.8 1.0 CD2 B:HIS81 2.9 37.9 1.0 CD2 A:HIS78 2.9 30.9 1.0 CE1 A:HIS78 3.0 34.4 1.0 CD B:GLU85 3.0 42.1 1.0 CE1 B:HIS81 3.1 38.4 1.0 OE1 B:GLU85 3.6 41.1 1.0 O B:HOH363 3.8 45.3 1.0 CG B:HIS81 4.1 35.5 1.0 ND1 A:HIS78 4.1 32.1 1.0 CG A:HIS78 4.1 30.6 1.0 ND1 B:HIS81 4.1 35.5 1.0 CG B:GLU85 4.2 43.2 1.0 O A:HOH353 4.3 35.0 1.0

Cobalt binding site 4 out of 4 in the The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 4 of The Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Co204 b:48.1 occ:1.00 O B:HOH369 1.8 48.1 1.0 O B:HOH320 1.8 43.1 1.0 O B:HOH343 1.8 46.7 1.0 O B:HOH336 1.8 42.4 1.0 NE2 B:HIS116 1.9 40.8 1.0 CD2 B:HIS116 2.9 38.7 1.0 CE1 B:HIS116 3.0 41.5 1.0 CG B:HIS116 4.1 36.6 1.0 ND1 B:HIS116 4.1 39.8 1.0 O B:HOH349 4.1 40.0 1.0 O B:HOH396 4.2 43.2 1.0 CB B:PRO120 4.4 38.1 1.0 O B:PHE123 4.5 36.8 1.0 CA B:PRO120 5.0 37.3 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