Iron 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:

Nickel

(Ni)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the The Ni-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin, PDB code: 7dgl:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe201 b:27.4 occ:1.00 FE A:HEM201 0.0 27.4 1.0 ND A:HEM201 1.9 30.3 1.0 O B:O201 1.9 28.7 1.0 NA A:HEM201 2.0 27.3 1.0 NE2 A:HIS93 2.0 26.3 1.0 NB A:HEM201 2.1 27.1 1.0 NC A:HEM201 2.1 26.2 1.0 C1D A:HEM201 2.9 31.4 1.0 C4D A:HEM201 2.9 31.2 1.0 C1B A:HEM201 3.0 25.9 1.0 C4C A:HEM201 3.0 28.6 1.0 C1A A:HEM201 3.0 29.7 1.0 CE1 A:HIS93 3.0 29.7 1.0 C4A A:HEM201 3.0 27.7 1.0 CD2 A:HIS93 3.0 30.1 1.0 C4B A:HEM201 3.0 26.4 1.0 C1C A:HEM201 3.1 27.2 1.0 CHD A:HEM201 3.4 29.0 1.0 CHA A:HEM201 3.4 30.9 1.0 CHB A:HEM201 3.4 27.1 1.0 CHC A:HEM201 3.4 27.3 1.0 ND1 A:HIS93 4.1 28.5 1.0 CG A:HIS93 4.2 26.4 1.0 C3D A:HEM201 4.2 31.1 1.0 C2D A:HEM201 4.2 33.7 1.0 NE2 B:HIS64 4.2 29.1 1.0 C3A A:HEM201 4.2 28.1 1.0 C2A A:HEM201 4.2 28.9 1.0 C2B A:HEM201 4.2 26.1 1.0 C3C A:HEM201 4.3 29.9 1.0 C2C A:HEM201 4.3 29.9 1.0 C3B A:HEM201 4.3 24.8 1.0 CG2 B:VAL68 4.7 24.8 1.0 CE1 B:HIS64 4.7 32.3 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe202 b:26.6 occ:1.00 FE B:HEM202 0.0 26.6 1.0 O A:O202 1.9 26.3 1.0 ND B:HEM202 1.9 27.7 1.0 NA B:HEM202 2.0 25.7 1.0 NE2 B:HIS93 2.0 28.5 1.0 NC B:HEM202 2.1 24.1 1.0 NB B:HEM202 2.1 26.9 1.0 C4D B:HEM202 3.0 29.0 1.0 C1D B:HEM202 3.0 28.7 1.0 C1A B:HEM202 3.0 29.5 1.0 CD2 B:HIS93 3.0 25.5 1.0 C4A B:HEM202 3.0 27.5 1.0 CE1 B:HIS93 3.0 25.4 1.0 C4C B:HEM202 3.0 26.3 1.0 C4B B:HEM202 3.1 28.0 1.0 C1B B:HEM202 3.1 30.8 1.0 C1C B:HEM202 3.1 25.7 1.0 CHA B:HEM202 3.4 26.8 1.0 CHD B:HEM202 3.4 30.9 1.0 CHB B:HEM202 3.4 27.1 1.0 CHC B:HEM202 3.5 24.9 1.0 ND1 B:HIS93 4.1 28.5 1.0 CG B:HIS93 4.2 26.1 1.0 C3D B:HEM202 4.2 30.4 1.0 C2D B:HEM202 4.2 30.4 1.0 C3A B:HEM202 4.2 29.1 1.0 C2A B:HEM202 4.2 29.7 1.0 C3C B:HEM202 4.3 26.5 1.0 C2C B:HEM202 4.3 25.0 1.0 NE2 A:HIS64 4.3 24.0 1.0 C3B B:HEM202 4.3 29.8 1.0 C2B B:HEM202 4.3 29.4 1.0 CG2 A:VAL68 4.6 27.6 1.0 CE1 A:HIS64 4.8 29.1 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