Iron in PDB 7dgm: The Dimeric Structure of K79H/G80A/H81A Myoglobin

The structure of The Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgm 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)	47.15 / 1.62
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.227, 62.897, 82.962, 90, 90, 90
R / Rfree (%)	20.2 / 22.3

The binding sites of Iron atom in the The Dimeric Structure of K79H/G80A/H81A Myoglobin (pdb code 7dgm). 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 Dimeric Structure of K79H/G80A/H81A Myoglobin, PDB code: 7dgm:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the The 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 Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:18.6 occ:1.00 FE A:HEM201 0.0 18.6 1.0 ND A:HEM201 1.9 19.2 1.0 NE2 A:HIS93 2.0 22.0 1.0 NA A:HEM201 2.0 18.6 1.0 O B:O201 2.0 21.0 1.0 NC A:HEM201 2.1 18.2 1.0 NB A:HEM201 2.1 17.7 1.0 C4D A:HEM201 2.9 20.1 1.0 C1D A:HEM201 3.0 20.8 1.0 CE1 A:HIS93 3.0 21.5 1.0 C1A A:HEM201 3.0 19.5 1.0 C4B A:HEM201 3.0 18.5 1.0 C4C A:HEM201 3.0 19.9 1.0 C4A A:HEM201 3.1 19.7 1.0 CD2 A:HIS93 3.1 20.7 1.0 C1B A:HEM201 3.1 18.2 1.0 C1C A:HEM201 3.1 18.9 1.0 CHA A:HEM201 3.4 19.2 1.0 CHD A:HEM201 3.4 19.4 1.0 CHC A:HEM201 3.5 18.2 1.0 CHB A:HEM201 3.5 18.0 1.0 ND1 A:HIS93 4.1 21.5 1.0 CG A:HIS93 4.2 21.0 1.0 C2D A:HEM201 4.2 19.5 1.0 C3D A:HEM201 4.2 21.2 1.0 C2A A:HEM201 4.2 18.7 1.0 C3A A:HEM201 4.2 19.1 1.0 C3C A:HEM201 4.2 20.7 1.0 C2C A:HEM201 4.3 20.0 1.0 C2B A:HEM201 4.3 16.7 1.0 C3B A:HEM201 4.3 17.2 1.0 NE2 B:HIS64 4.3 23.1 1.0 CG2 B:VAL68 4.7 19.3 1.0 CE1 B:HIS64 4.8 23.2 1.0 CD2 A:HIS97 4.9 23.8 1.0

Iron binding site 2 out of 2 in the The 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 Dimeric Structure of K79H/G80A/H81A Myoglobin within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe202 b:19.8 occ:1.00 FE B:HEM202 0.0 19.8 1.0 ND B:HEM202 1.9 20.6 1.0 NE2 B:HIS93 2.0 23.5 1.0 NA B:HEM202 2.0 21.9 1.0 O A:O202 2.0 24.5 1.0 NC B:HEM202 2.1 19.6 1.0 NB B:HEM202 2.1 18.2 1.0 CE1 B:HIS93 2.9 23.4 1.0 C1D B:HEM202 3.0 22.7 1.0 C4D B:HEM202 3.0 24.6 1.0 C1A B:HEM202 3.0 25.4 1.0 C4C B:HEM202 3.0 20.2 1.0 C4A B:HEM202 3.0 20.9 1.0 C1B B:HEM202 3.1 18.9 1.0 CD2 B:HIS93 3.1 21.7 1.0 C4B B:HEM202 3.1 19.1 1.0 C1C B:HEM202 3.1 18.3 1.0 CHD B:HEM202 3.4 22.2 1.0 CHA B:HEM202 3.4 23.5 1.0 CHB B:HEM202 3.5 19.3 1.0 CHC B:HEM202 3.5 17.6 1.0 ND1 B:HIS93 4.1 23.1 1.0 CG B:HIS93 4.2 22.1 1.0 C2A B:HEM202 4.2 25.2 1.0 C3D B:HEM202 4.2 25.8 1.0 C3A B:HEM202 4.2 23.4 1.0 C2D B:HEM202 4.2 24.8 1.0 C3C B:HEM202 4.3 18.8 1.0 NE2 A:HIS64 4.3 26.4 1.0 C2C B:HEM202 4.3 18.9 1.0 C2B B:HEM202 4.3 18.2 1.0 C3B B:HEM202 4.3 17.6 1.0 CE1 A:HIS64 4.7 27.0 1.0 CG2 A:VAL68 4.8 22.7 1.0 CD2 B:HIS97 4.9 27.1 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