Iron in PDB 7e98: Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% Oxygen Saturation

The structure of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% Oxygen Saturation, PDB code: 7e98 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)	47.84 / 2.20
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	112.245, 112.245, 271.388, 90, 90, 120
R / Rfree (%)	18.8 / 21.9

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% Oxygen Saturation (pdb code 7e98). 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 21% Oxygen Saturation, PDB code: 7e98:
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 21% 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 21% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:36.1 occ:1.00 FE A:HEM201 0.0 36.1 1.0 O1 A:OXY202 1.8 40.0 0.2 NC A:HEM201 2.0 41.0 1.0 ND A:HEM201 2.1 40.6 1.0 NB A:HEM201 2.1 39.9 1.0 NA A:HEM201 2.1 38.9 1.0 NE2 A:HIS94 2.2 43.0 1.0 O2 A:OXY202 2.9 38.1 0.2 C4C A:HEM201 3.0 37.8 1.0 C1C A:HEM201 3.0 40.5 1.0 C1D A:HEM201 3.0 41.3 1.0 C1B A:HEM201 3.1 40.9 1.0 C4D A:HEM201 3.1 41.5 1.0 C4B A:HEM201 3.1 38.7 1.0 C4A A:HEM201 3.1 36.1 1.0 C1A A:HEM201 3.1 38.6 1.0 CE1 A:HIS94 3.1 39.6 1.0 CD2 A:HIS94 3.2 41.5 1.0 CHD A:HEM201 3.4 38.4 1.0 CHC A:HEM201 3.4 40.0 1.0 CHB A:HEM201 3.5 36.1 1.0 CHA A:HEM201 3.5 35.0 1.0 C3C A:HEM201 4.3 37.2 1.0 C2C A:HEM201 4.3 35.6 1.0 C2D A:HEM201 4.3 41.9 1.0 ND1 A:HIS94 4.3 37.1 1.0 C3D A:HEM201 4.3 40.5 1.0 C2B A:HEM201 4.3 41.0 1.0 C3B A:HEM201 4.3 33.8 1.0 C3A A:HEM201 4.3 38.8 1.0 CG A:HIS94 4.3 46.9 1.0 C2A A:HEM201 4.3 37.1 1.0 NH1 A:ARG97 4.3 45.6 1.0 CG2 A:VAL66 4.4 29.3 1.0 CG1 A:VAL66 4.7 31.3 1.0 O A:HOH327 4.9 41.5 1.0

Iron binding site 2 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% 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 21% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:38.1 occ:1.00 FE B:HEM200 0.0 38.1 1.0 O1 B:OXY201 1.8 37.0 0.1 NC B:HEM200 2.0 39.1 1.0 ND B:HEM200 2.1 35.7 1.0 NB B:HEM200 2.1 35.4 1.0 NA B:HEM200 2.1 34.9 1.0 NE2 B:HIS94 2.2 39.2 1.0 O2 B:OXY201 2.9 37.2 0.1 CD2 B:HIS94 3.0 37.3 1.0 C4C B:HEM200 3.0 37.5 1.0 C1D B:HEM200 3.0 39.3 1.0 C1C B:HEM200 3.1 39.3 1.0 C1B B:HEM200 3.1 35.2 1.0 C4B B:HEM200 3.1 33.9 1.0 C4D B:HEM200 3.1 36.6 1.0 C4A B:HEM200 3.1 34.3 1.0 C1A B:HEM200 3.1 34.9 1.0 CE1 B:HIS94 3.3 39.5 1.0 CHD B:HEM200 3.4 37.7 1.0 CHB B:HEM200 3.4 32.4 1.0 CHC B:HEM200 3.4 38.8 1.0 CHA B:HEM200 3.5 37.5 1.0 CG B:HIS94 4.2 40.5 1.0 C2D B:HEM200 4.3 43.7 1.0 C3C B:HEM200 4.3 38.5 1.0 C2C B:HEM200 4.3 37.3 1.0 C3D B:HEM200 4.3 41.6 1.0 CG2 B:VAL66 4.3 32.0 1.0 C2B B:HEM200 4.3 33.8 1.0 C3B B:HEM200 4.3 31.4 1.0 C3A B:HEM200 4.3 36.9 1.0 ND1 B:HIS94 4.3 35.8 1.0 C2A B:HEM200 4.3 38.5 1.0 CG1 B:VAL66 4.6 33.2 1.0

Iron binding site 3 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% 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 21% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:47.3 occ:1.00 FE C:HEM200 0.0 47.3 1.0 O1 C:OXY201 1.8 50.9 0.3 NC C:HEM200 2.0 52.5 1.0 ND C:HEM200 2.1 55.8 1.0 NB C:HEM200 2.1 53.4 1.0 NA C:HEM200 2.1 50.6 1.0 NE2 C:HIS98 2.2 40.3 1.0 O2 C:OXY201 2.9 51.5 0.3 C4C C:HEM200 3.0 53.7 1.0 C1D C:HEM200 3.0 56.1 1.0 C1B C:HEM200 3.1 49.3 1.0 C4A C:HEM200 3.1 49.5 1.0 C1C C:HEM200 3.1 49.3 1.0 C4B C:HEM200 3.1 49.9 1.0 C4D C:HEM200 3.1 58.6 1.0 C1A C:HEM200 3.1 54.3 1.0 CD2 C:HIS98 3.2 45.5 1.0 CE1 C:HIS98 3.2 39.1 1.0 CHD C:HEM200 3.4 53.5 1.0 CHB C:HEM200 3.4 48.5 1.0 CHC C:HEM200 3.5 47.3 1.0 CHA C:HEM200 3.5 56.7 1.0 NH2 C:ARG101 4.1 53.6 1.0 C3C C:HEM200 4.3 52.4 1.0 C2D C:HEM200 4.3 61.5 1.0 C2C C:HEM200 4.3 52.9 1.0 C2B C:HEM200 4.3 48.8 1.0 ND1 C:HIS98 4.3 42.8 1.0 C3A C:HEM200 4.3 49.5 1.0 C3D C:HEM200 4.3 61.5 1.0 C3B C:HEM200 4.3 50.4 1.0 CG C:HIS98 4.3 51.5 1.0 C2A C:HEM200 4.3 54.2 1.0 CG1 C:VAL70 4.5 37.7 1.0 CG2 C:VAL70 4.6 37.9 1.0

Iron binding site 4 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 21% 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 21% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:38.9 occ:1.00 FE D:HEM200 0.0 38.9 1.0 O1 D:OXY201 1.8 41.9 0.1 NC D:HEM200 2.0 40.5 1.0 ND D:HEM200 2.1 44.9 1.0 NB D:HEM200 2.1 39.0 1.0 NA D:HEM200 2.1 40.9 1.0 NE2 D:HIS96 2.2 40.4 1.0 O2 D:OXY201 2.8 42.8 0.1 C4C D:HEM200 3.0 41.0 1.0 C1D D:HEM200 3.1 47.6 1.0 C1C D:HEM200 3.1 42.6 1.0 C4B D:HEM200 3.1 37.1 1.0 C1B D:HEM200 3.1 37.5 1.0 C4D D:HEM200 3.1 42.5 1.0 C4A D:HEM200 3.1 38.5 1.0 C1A D:HEM200 3.1 43.4 1.0 CD2 D:HIS96 3.2 41.7 1.0 CE1 D:HIS96 3.2 41.4 1.0 CHD D:HEM200 3.4 42.8 1.0 CHC D:HEM200 3.4 36.4 1.0 CHB D:HEM200 3.5 34.2 1.0 CHA D:HEM200 3.5 44.4 1.0 C2C D:HEM200 4.3 42.3 1.0 C3C D:HEM200 4.3 48.8 1.0 C2D D:HEM200 4.3 47.6 1.0 ND1 D:HIS96 4.3 41.4 1.0 C3D D:HEM200 4.3 43.0 1.0 C3B D:HEM200 4.3 35.3 1.0 CG D:HIS96 4.3 45.3 1.0 C2B D:HEM200 4.3 39.4 1.0 C3A D:HEM200 4.3 38.5 1.0 C2A D:HEM200 4.3 39.3 1.0 CG2 D:VAL68 4.5 36.6 1.0 CG1 D:VAL68 4.7 31.8 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