Nickel in PDB 7dgl: The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin

The structure of The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin, PDB code: 7dgl 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)	46.93 / 1.91
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.819, 63.276, 83.267, 90, 90, 90
R / Rfree (%)	20.9 / 26.2

The structure of The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

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

Nickel binding site 1 out of 2 in the The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni203 b:38.1 occ:1.00 OE2 A:GLU85 1.9 36.0 1.0 O B:HOH334 1.9 34.9 1.0 O A:HOH352 2.0 45.1 1.0 NE2 B:HIS78 2.1 35.4 1.0 O B:HOH330 2.1 31.4 1.0 NE2 A:HIS81 2.1 39.3 1.0 CD A:GLU85 3.0 43.8 1.0 CE1 B:HIS78 3.0 35.3 1.0 CD2 A:HIS81 3.1 40.9 1.0 CD2 B:HIS78 3.1 30.1 1.0 CE1 A:HIS81 3.2 41.0 1.0 OE1 A:GLU85 3.5 40.5 1.0 ND1 B:HIS78 4.1 31.6 1.0 CG B:HIS78 4.2 31.5 1.0 O B:HOH336 4.2 33.3 1.0 CG A:HIS81 4.2 38.2 1.0 ND1 A:HIS81 4.2 39.3 1.0 CG A:GLU85 4.3 42.4 1.0 O A:HOH323 4.8 38.6 1.0 CB A:GLU85 4.9 40.3 1.0

Nickel binding site 2 out of 2 in the The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni203 b:34.5 occ:1.00 O B:HOH345 2.0 35.9 1.0 O B:HOH305 2.0 35.9 1.0 OE1 B:GLU85 2.0 34.7 1.0 O B:HOH317 2.0 45.2 1.0 NE2 B:HIS81 2.0 38.0 1.0 NE2 A:HIS78 2.1 29.7 1.0 CD2 B:HIS81 2.9 32.9 1.0 CD B:GLU85 3.0 39.0 1.0 CE1 A:HIS78 3.0 34.2 1.0 CD2 A:HIS78 3.1 28.1 1.0 CE1 B:HIS81 3.1 35.8 1.0 OE2 B:GLU85 3.3 35.9 1.0 O A:HOH337 4.1 30.8 1.0 CG B:HIS81 4.1 35.3 1.0 ND1 A:HIS78 4.1 32.2 1.0 ND1 B:HIS81 4.2 34.2 1.0 CG A:HIS78 4.2 28.1 1.0 CG B:GLU85 4.3 37.5 1.0 CB B:GLU85 4.9 38.0 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