Iron in PDB 7e96: Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation

The structure of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation, PDB code: 7e96 was solved by N.Numoto, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.61 / 2.40
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.213, 110.213, 274.656, 90, 90, 120
R / Rfree (%)	19.2 / 23.9

The structure of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation also contains other interesting chemical elements:

Calcium

(Ca)

1 atom

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation (pdb code 7e96). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation, PDB code: 7e96:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:51.2 occ:1.00 FE A:HEM201 0.0 51.2 1.0 O1 A:OXY202 1.8 51.0 0.8 ND A:HEM201 2.0 53.5 1.0 NB A:HEM201 2.0 48.4 1.0 NE2 A:HIS94 2.0 52.1 1.0 NA A:HEM201 2.0 49.2 1.0 NC A:HEM201 2.1 52.5 1.0 O2 A:OXY202 2.8 48.4 0.8 CE1 A:HIS94 3.0 54.6 1.0 C1D A:HEM201 3.0 53.3 1.0 C4A A:HEM201 3.1 47.9 1.0 C4B A:HEM201 3.1 50.3 1.0 C4D A:HEM201 3.1 51.9 1.0 C1C A:HEM201 3.1 51.9 1.0 C4C A:HEM201 3.1 51.8 1.0 C1B A:HEM201 3.1 49.5 1.0 C1A A:HEM201 3.1 51.2 1.0 CD2 A:HIS94 3.1 54.5 1.0 CHC A:HEM201 3.4 51.8 1.0 CHD A:HEM201 3.4 54.1 1.0 CHB A:HEM201 3.4 47.4 1.0 CHA A:HEM201 3.4 49.6 1.0 ND1 A:HIS94 4.1 55.2 1.0 CG A:HIS94 4.2 57.6 1.0 C2D A:HEM201 4.3 54.7 1.0 C3D A:HEM201 4.3 54.5 1.0 C3B A:HEM201 4.3 49.2 1.0 C3A A:HEM201 4.3 49.7 1.0 C3C A:HEM201 4.3 49.1 1.0 C2B A:HEM201 4.3 49.7 1.0 C2C A:HEM201 4.3 50.2 1.0 C2A A:HEM201 4.3 48.2 1.0 CG2 A:VAL66 4.5 47.5 1.0 CE1 A:HIS62 4.9 51.5 1.0

Iron binding site 2 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:43.0 occ:1.00 FE B:HEM200 0.0 43.0 1.0 O1 B:OXY201 1.8 46.1 0.7 ND B:HEM200 2.0 43.6 1.0 NC B:HEM200 2.0 47.0 1.0 NB B:HEM200 2.0 43.7 1.0 NE2 B:HIS94 2.0 48.1 1.0 NA B:HEM200 2.1 46.8 1.0 O2 B:OXY201 2.9 44.3 0.7 C1D B:HEM200 3.0 47.2 1.0 CE1 B:HIS94 3.0 46.0 1.0 CD2 B:HIS94 3.0 48.5 1.0 C4C B:HEM200 3.0 45.4 1.0 C4D B:HEM200 3.0 47.3 1.0 C4B B:HEM200 3.1 42.9 1.0 C1B B:HEM200 3.1 44.7 1.0 C1C B:HEM200 3.1 45.1 1.0 C4A B:HEM200 3.1 44.0 1.0 C1A B:HEM200 3.1 43.8 1.0 CHD B:HEM200 3.4 48.1 1.0 CHB B:HEM200 3.4 41.8 1.0 CHC B:HEM200 3.4 44.8 1.0 CHA B:HEM200 3.5 47.5 1.0 ND1 B:HIS94 4.1 46.5 1.0 CG B:HIS94 4.1 50.0 1.0 C2D B:HEM200 4.2 47.1 1.0 C3D B:HEM200 4.2 47.8 1.0 C3C B:HEM200 4.3 43.7 1.0 CG2 B:VAL66 4.3 41.5 1.0 C2C B:HEM200 4.3 48.5 1.0 C3B B:HEM200 4.3 40.1 1.0 C2B B:HEM200 4.3 41.3 1.0 C3A B:HEM200 4.3 45.6 1.0 C2A B:HEM200 4.3 46.1 1.0 CE1 B:HIS62 4.6 45.4 1.0

Iron binding site 3 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:48.9 occ:1.00 FE C:HEM200 0.0 48.9 1.0 O1 C:OXY201 1.8 49.3 0.7 NC C:HEM200 2.0 50.6 1.0 NA C:HEM200 2.0 50.7 1.0 NB C:HEM200 2.0 51.7 1.0 NE2 C:HIS98 2.1 45.5 1.0 ND C:HEM200 2.1 53.0 1.0 O2 C:OXY201 3.0 48.9 0.7 CE1 C:HIS98 3.0 49.2 1.0 C1C C:HEM200 3.0 52.0 1.0 C4B C:HEM200 3.0 49.4 1.0 C4C C:HEM200 3.0 50.3 1.0 C1A C:HEM200 3.1 51.0 1.0 C4A C:HEM200 3.1 50.7 1.0 C1B C:HEM200 3.1 49.4 1.0 C1D C:HEM200 3.1 50.5 1.0 C4D C:HEM200 3.1 51.7 1.0 CD2 C:HIS98 3.1 50.0 1.0 CHC C:HEM200 3.4 51.0 1.0 CHB C:HEM200 3.4 47.3 1.0 CHD C:HEM200 3.5 53.8 1.0 CHA C:HEM200 3.5 50.5 1.0 ND1 C:HIS98 4.1 46.7 1.0 CG C:HIS98 4.2 50.9 1.0 C2C C:HEM200 4.2 54.3 1.0 C3C C:HEM200 4.3 53.1 1.0 C3B C:HEM200 4.3 47.2 1.0 C2A C:HEM200 4.3 50.6 1.0 C2B C:HEM200 4.3 48.4 1.0 C3A C:HEM200 4.3 48.4 1.0 C3D C:HEM200 4.3 53.3 1.0 C2D C:HEM200 4.3 53.3 1.0 CG2 C:VAL70 4.5 49.0 1.0 CE1 C:HIS66 4.8 50.4 1.0

Iron binding site 4 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:47.2 occ:1.00 FE D:HEM200 0.0 47.2 1.0 O1 D:OXY201 1.8 49.6 0.6 ND D:HEM200 2.0 45.6 1.0 NA D:HEM200 2.1 47.2 1.0 NC D:HEM200 2.1 49.1 1.0 NE2 D:HIS96 2.1 52.2 1.0 NB D:HEM200 2.1 46.4 1.0 O2 D:OXY201 2.8 49.7 0.6 CD2 D:HIS96 3.0 45.6 1.0 C4D D:HEM200 3.0 48.8 1.0 C1D D:HEM200 3.0 48.9 1.0 C1A D:HEM200 3.1 50.1 1.0 C4C D:HEM200 3.1 52.5 1.0 C1C D:HEM200 3.1 52.0 1.0 CE1 D:HIS96 3.1 44.9 1.0 C4A D:HEM200 3.1 46.7 1.0 C4B D:HEM200 3.1 45.1 1.0 C1B D:HEM200 3.1 44.5 1.0 CHA D:HEM200 3.4 60.0 1.0 CHD D:HEM200 3.4 63.3 1.0 CHC D:HEM200 3.4 43.3 1.0 CHB D:HEM200 3.4 45.8 1.0 ND1 D:HIS96 4.2 42.9 1.0 CG D:HIS96 4.2 47.5 1.0 C3D D:HEM200 4.3 56.6 1.0 C2D D:HEM200 4.3 56.9 1.0 C2C D:HEM200 4.3 48.4 1.0 C3C D:HEM200 4.3 59.8 1.0 C2A D:HEM200 4.3 52.4 1.0 C3A D:HEM200 4.3 52.6 1.0 C3B D:HEM200 4.3 49.6 1.0 C2B D:HEM200 4.3 49.1 1.0 NE2 D:GLN64 4.7 55.2 1.0 CG2 D:VAL68 4.7 48.7 1.0

N.Numoto, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito. Coarse Snapshots of Oxygen-Dissociation Intermediates of A Giant Hemoglobin Elucidated By Determining the Oxygen Saturation in Individual Subunits in the Crystalline State. Iucrj 2021.
ISSN: ESSN 2052-2525
DOI: 10.1107/S2052252521009386