Iron 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:

Cobalt

(Co)

2 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the The Co-Bound Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgn:
Jump to Iron binding site number: 1; 2;

Iron 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 Iron with other atoms in the Fe 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:Fe201 b:34.1 occ:1.00 FE A:HEM201 0.0 34.1 1.0 ND A:HEM201 1.9 37.5 1.0 O B:O201 2.0 27.5 1.0 NA A:HEM201 2.0 38.3 1.0 NB A:HEM201 2.1 32.0 1.0 NC A:HEM201 2.1 31.7 1.0 NE2 A:HIS93 2.1 32.9 1.0 C1D A:HEM201 2.9 34.8 1.0 C4D A:HEM201 3.0 35.5 1.0 C4C A:HEM201 3.0 34.0 1.0 C1A A:HEM201 3.0 36.2 1.0 C4A A:HEM201 3.0 35.1 1.0 CE1 A:HIS93 3.0 36.1 1.0 C1B A:HEM201 3.0 33.2 1.0 C4B A:HEM201 3.0 34.3 1.0 C1C A:HEM201 3.1 35.0 1.0 CD2 A:HIS93 3.1 39.9 1.0 CHD A:HEM201 3.4 31.4 1.0 CHB A:HEM201 3.4 37.6 1.0 CHA A:HEM201 3.4 35.1 1.0 CHC A:HEM201 3.5 32.5 1.0 ND1 A:HIS93 4.1 38.3 1.0 C3A A:HEM201 4.2 34.5 1.0 C2A A:HEM201 4.2 35.8 1.0 C2D A:HEM201 4.2 36.1 1.0 C3D A:HEM201 4.2 33.1 1.0 CG A:HIS93 4.2 38.6 1.0 C3C A:HEM201 4.2 37.2 1.0 C2B A:HEM201 4.2 34.3 1.0 C3B A:HEM201 4.3 33.9 1.0 C2C A:HEM201 4.3 37.4 1.0 NE2 B:HIS64 4.4 34.8 1.0 CG2 B:VAL68 4.5 36.3 1.0 CE1 B:HIS64 4.7 38.8 1.0 CD2 A:HIS97 4.9 39.8 1.0

Iron 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 Iron with other atoms in the Fe 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:Fe202 b:35.1 occ:1.00 FE B:HEM202 0.0 35.1 1.0 ND B:HEM202 1.9 38.1 1.0 O A:O202 2.0 33.3 1.0 NA B:HEM202 2.0 38.0 1.0 NB B:HEM202 2.1 29.1 1.0 NE2 B:HIS93 2.1 37.0 1.0 NC B:HEM202 2.1 34.5 1.0 C1D B:HEM202 2.9 40.2 1.0 C4D B:HEM202 2.9 40.0 1.0 CE1 B:HIS93 3.0 39.2 1.0 C4C B:HEM202 3.0 34.2 1.0 C1A B:HEM202 3.0 35.3 1.0 C1B B:HEM202 3.0 32.4 1.0 C4B B:HEM202 3.0 31.4 1.0 C4A B:HEM202 3.0 35.2 1.0 CD2 B:HIS93 3.1 35.2 1.0 C1C B:HEM202 3.2 29.2 1.0 CHD B:HEM202 3.3 38.4 1.0 CHA B:HEM202 3.4 31.8 1.0 CHB B:HEM202 3.4 31.6 1.0 CHC B:HEM202 3.5 27.2 1.0 C2D B:HEM202 4.1 43.8 1.0 ND1 B:HIS93 4.1 38.8 1.0 C3D B:HEM202 4.2 45.2 1.0 C2A B:HEM202 4.2 37.9 1.0 C3A B:HEM202 4.2 38.1 1.0 CG B:HIS93 4.2 34.6 1.0 C2B B:HEM202 4.3 30.9 1.0 C3B B:HEM202 4.3 30.1 1.0 C3C B:HEM202 4.3 34.1 1.0 C2C B:HEM202 4.3 28.3 1.0 NE2 A:HIS64 4.4 41.2 1.0 CG2 A:VAL68 4.6 31.5 1.0 CE1 A:HIS64 4.8 46.2 1.0 CD2 B:HIS97 4.9 50.9 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