Iron 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:

Cobalt

(Co)

4 atoms

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

Iron binding site 1 out of 2 in the The Co-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 Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:27.3 occ:1.00 FE A:HEM201 0.0 27.3 1.0 NE2 A:HIS93 1.9 28.6 1.0 ND A:HEM201 1.9 25.7 1.0 NA A:HEM201 2.0 26.2 1.0 O B:O201 2.0 27.8 1.0 NC A:HEM201 2.0 27.0 1.0 NB A:HEM201 2.0 23.7 1.0 CE1 A:HIS93 2.9 29.1 1.0 C1D A:HEM201 2.9 28.0 1.0 C4D A:HEM201 3.0 28.9 1.0 C1B A:HEM201 3.0 26.6 1.0 C4B A:HEM201 3.0 26.1 1.0 C4C A:HEM201 3.0 27.1 1.0 C1A A:HEM201 3.0 26.0 1.0 C4A A:HEM201 3.1 26.0 1.0 C1C A:HEM201 3.1 26.0 1.0 CD2 A:HIS93 3.1 29.9 1.0 CHD A:HEM201 3.3 27.4 1.0 CHA A:HEM201 3.4 28.3 1.0 CHC A:HEM201 3.4 26.9 1.0 CHB A:HEM201 3.4 26.4 1.0 ND1 A:HIS93 4.0 27.5 1.0 CG A:HIS93 4.2 30.4 1.0 C2D A:HEM201 4.2 27.5 1.0 NE2 B:HIS64 4.2 29.2 1.0 C2B A:HEM201 4.2 25.9 1.0 C3C A:HEM201 4.2 28.8 1.0 C3D A:HEM201 4.2 28.5 1.0 C2A A:HEM201 4.3 26.5 1.0 C2C A:HEM201 4.3 28.7 1.0 C3B A:HEM201 4.3 25.4 1.0 C3A A:HEM201 4.3 27.3 1.0 CG2 B:VAL68 4.6 27.4 1.0 CE1 B:HIS64 4.7 30.9 1.0 CD2 A:HIS97 5.0 32.9 1.0

Iron binding site 2 out of 2 in the The Co-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 Co-Bound Dimeric Structure of K78H/G80A/H82A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:25.8 occ:1.00 FE B:HEM202 0.0 25.8 1.0 ND B:HEM202 1.9 24.4 1.0 NA B:HEM202 2.0 26.1 1.0 NE2 B:HIS93 2.0 25.7 1.0 NC B:HEM202 2.0 23.8 1.0 O A:O202 2.0 25.9 1.0 NB B:HEM202 2.0 23.4 1.0 C1D B:HEM202 2.9 25.4 1.0 C4B B:HEM202 2.9 25.0 1.0 CE1 B:HIS93 3.0 25.6 1.0 C4D B:HEM202 3.0 27.6 1.0 C4C B:HEM202 3.0 24.4 1.0 CD2 B:HIS93 3.0 24.0 1.0 C1B B:HEM202 3.0 25.7 1.0 C1A B:HEM202 3.0 26.0 1.0 C4A B:HEM202 3.0 26.8 1.0 C1C B:HEM202 3.0 23.8 1.0 CHD B:HEM202 3.4 25.2 1.0 CHC B:HEM202 3.4 23.5 1.0 CHB B:HEM202 3.5 25.4 1.0 CHA B:HEM202 3.5 25.9 1.0 ND1 B:HIS93 4.1 27.9 1.0 C2D B:HEM202 4.1 25.9 1.0 CG B:HIS93 4.2 27.2 1.0 C3D B:HEM202 4.2 27.4 1.0 C3C B:HEM202 4.2 23.8 1.0 C2B B:HEM202 4.2 23.9 1.0 C3A B:HEM202 4.2 26.6 1.0 C2C B:HEM202 4.2 23.9 1.0 C2A B:HEM202 4.2 28.3 1.0 C3B B:HEM202 4.2 24.2 1.0 NE2 A:HIS64 4.3 28.1 1.0 CG2 A:VAL68 4.6 27.9 1.0 CE1 A:HIS64 4.8 30.1 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