Iron in PDB 7e99: Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% Oxygen Saturation

The structure of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% Oxygen Saturation, PDB code: 7e99 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)	47.30 / 2.10
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	110.925, 110.925, 271.047, 90, 90, 120
R / Rfree (%)	18.1 / 22

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% Oxygen Saturation (pdb code 7e99). 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 13% Oxygen Saturation, PDB code: 7e99:
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 13% 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 13% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:35.5 occ:1.00 FE A:HEM200 0.0 35.5 1.0 O1 A:OXY201 1.8 35.7 0.0 NC A:HEM200 2.0 38.6 1.0 ND A:HEM200 2.1 38.5 1.0 NB A:HEM200 2.1 38.5 1.0 NA A:HEM200 2.1 37.0 1.0 NE2 A:HIS94 2.2 37.4 1.0 O2 A:OXY201 2.9 35.4 0.0 C4C A:HEM200 3.0 35.9 1.0 C1D A:HEM200 3.0 35.5 1.0 C1C A:HEM200 3.0 36.3 1.0 C1B A:HEM200 3.1 35.5 1.0 C4A A:HEM200 3.1 32.0 1.0 C4B A:HEM200 3.1 37.9 1.0 C4D A:HEM200 3.1 37.3 1.0 C1A A:HEM200 3.2 36.9 1.0 CE1 A:HIS94 3.2 38.0 1.0 CD2 A:HIS94 3.2 40.1 1.0 CHD A:HEM200 3.4 35.6 1.0 CHC A:HEM200 3.4 36.2 1.0 CHB A:HEM200 3.4 35.1 1.0 CHA A:HEM200 3.5 36.2 1.0 C3C A:HEM200 4.2 33.2 1.0 C2C A:HEM200 4.3 34.5 1.0 C2D A:HEM200 4.3 38.5 1.0 ND1 A:HIS94 4.3 35.6 1.0 C3D A:HEM200 4.3 36.7 1.0 C2B A:HEM200 4.3 38.1 1.0 C3B A:HEM200 4.3 35.4 1.0 CG A:HIS94 4.3 39.4 1.0 C3A A:HEM200 4.3 32.4 1.0 C2A A:HEM200 4.4 34.3 1.0 NH1 A:ARG97 4.4 41.1 1.0 CG2 A:VAL66 4.5 27.4 1.0 CG1 A:VAL66 4.9 31.7 1.0

Iron binding site 2 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% 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 13% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:32.7 occ:1.00 FE B:HEM200 0.0 32.7 1.0 O1 B:OXY201 1.8 31.7 0.1 NC B:HEM200 2.0 34.2 1.0 ND B:HEM200 2.0 35.5 1.0 NB B:HEM200 2.1 32.4 1.0 NA B:HEM200 2.1 33.6 1.0 NE2 B:HIS94 2.2 34.5 1.0 O2 B:OXY201 2.9 31.2 0.1 C4C B:HEM200 3.0 30.0 1.0 C1D B:HEM200 3.0 31.6 1.0 C1C B:HEM200 3.0 34.5 1.0 CD2 B:HIS94 3.0 31.3 1.0 C4D B:HEM200 3.1 35.0 1.0 C4B B:HEM200 3.1 30.5 1.0 C4A B:HEM200 3.1 28.7 1.0 C1B B:HEM200 3.1 29.6 1.0 C1A B:HEM200 3.1 33.4 1.0 CE1 B:HIS94 3.3 35.4 1.0 CHD B:HEM200 3.4 30.6 1.0 CHC B:HEM200 3.4 31.4 1.0 CHA B:HEM200 3.5 31.9 1.0 CHB B:HEM200 3.5 30.3 1.0 CG2 B:VAL66 4.2 28.7 1.0 CG B:HIS94 4.2 34.1 1.0 C2D B:HEM200 4.3 37.8 1.0 C2C B:HEM200 4.3 27.1 1.0 C3C B:HEM200 4.3 30.2 1.0 C3D B:HEM200 4.3 35.1 1.0 ND1 B:HIS94 4.3 29.4 1.0 C3B B:HEM200 4.3 28.7 1.0 C2B B:HEM200 4.3 27.5 1.0 C3A B:HEM200 4.3 30.6 1.0 C2A B:HEM200 4.3 32.1 1.0 CG1 B:VAL66 4.7 28.9 1.0

Iron binding site 3 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% 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 13% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:38.2 occ:1.00 FE C:HEM200 0.0 38.2 1.0 O1 C:OXY201 1.8 39.4 0.1 NB C:HEM200 2.1 43.1 1.0 ND C:HEM200 2.1 41.2 1.0 NC C:HEM200 2.1 41.9 1.0 NA C:HEM200 2.1 42.0 1.0 NE2 C:HIS98 2.2 34.9 1.0 O2 C:OXY201 2.9 39.3 0.1 C1B C:HEM200 3.1 40.1 1.0 C4A C:HEM200 3.1 41.1 1.0 C4C C:HEM200 3.1 38.9 1.0 C1D C:HEM200 3.1 41.7 1.0 C4D C:HEM200 3.1 42.9 1.0 C4B C:HEM200 3.1 35.5 1.0 C1C C:HEM200 3.1 41.8 1.0 CD2 C:HIS98 3.1 35.2 1.0 C1A C:HEM200 3.1 42.4 1.0 CE1 C:HIS98 3.2 37.0 1.0 CHB C:HEM200 3.4 41.2 1.0 CHD C:HEM200 3.4 40.8 1.0 CHA C:HEM200 3.5 41.4 1.0 CHC C:HEM200 3.5 39.9 1.0 NH2 C:ARG101 4.2 39.8 1.0 CG C:HIS98 4.3 34.2 1.0 C2B C:HEM200 4.3 39.8 1.0 C3A C:HEM200 4.3 40.1 1.0 C2D C:HEM200 4.3 42.0 1.0 C3C C:HEM200 4.3 40.5 1.0 C3D C:HEM200 4.3 45.6 1.0 C3B C:HEM200 4.3 36.5 1.0 C2C C:HEM200 4.3 42.4 1.0 C2A C:HEM200 4.3 40.9 1.0 ND1 C:HIS98 4.3 34.3 1.0 CG2 C:VAL70 4.5 34.5 1.0 CG1 C:VAL70 4.5 32.2 1.0 O C:HOH343 4.7 40.3 1.0

Iron binding site 4 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 13% 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 13% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:36.7 occ:1.00 FE D:HEM200 0.0 36.7 1.0 O1 D:OXY201 1.8 38.4 0.1 NB D:HEM200 2.0 34.6 1.0 NC D:HEM200 2.0 38.3 1.0 NA D:HEM200 2.1 38.5 1.0 ND D:HEM200 2.1 36.6 1.0 NE2 D:HIS96 2.2 39.5 1.0 O2 D:OXY201 2.9 38.4 0.1 C1B D:HEM200 3.1 35.9 1.0 C4C D:HEM200 3.1 41.0 1.0 C4B D:HEM200 3.1 35.4 1.0 C1C D:HEM200 3.1 37.8 1.0 C4A D:HEM200 3.1 35.8 1.0 CD2 D:HIS96 3.1 39.0 1.0 C1D D:HEM200 3.1 41.7 1.0 C1A D:HEM200 3.1 34.9 1.0 C4D D:HEM200 3.1 39.9 1.0 CE1 D:HIS96 3.3 37.4 1.0 CHB D:HEM200 3.4 36.1 1.0 CHD D:HEM200 3.4 40.3 1.0 CHC D:HEM200 3.4 35.4 1.0 CHA D:HEM200 3.5 37.5 1.0 CG2 D:VAL68 4.3 38.6 1.0 CG D:HIS96 4.3 42.1 1.0 C2B D:HEM200 4.3 34.2 1.0 C2C D:HEM200 4.3 39.5 1.0 C3C D:HEM200 4.3 43.1 1.0 C3B D:HEM200 4.3 32.7 1.0 C3A D:HEM200 4.3 36.0 1.0 C2D D:HEM200 4.3 45.5 1.0 C2A D:HEM200 4.3 37.4 1.0 ND1 D:HIS96 4.3 36.6 1.0 C3D D:HEM200 4.3 43.0 1.0 CG1 D:VAL68 4.6 33.1 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