Iron in PDB 7e97: Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% Oxygen Saturation

The structure of Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% Oxygen Saturation, PDB code: 7e97 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)	47.40 / 2.70
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	111.042, 111.042, 272.415, 90, 90, 120
R / Rfree (%)	20.6 / 25.2

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% Oxygen Saturation (pdb code 7e97). 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 58% Oxygen Saturation, PDB code: 7e97:
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 58% 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 58% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:63.3 occ:1.00 FE A:HEM200 0.0 63.3 1.0 O1 A:OXY201 1.8 66.5 0.4 NC A:HEM200 2.0 68.0 1.0 ND A:HEM200 2.1 66.1 1.0 NB A:HEM200 2.1 67.3 1.0 NA A:HEM200 2.1 67.6 1.0 NE2 A:HIS94 2.2 66.2 1.0 O2 A:OXY201 2.9 66.0 0.4 C4C A:HEM200 3.0 67.3 1.0 C1C A:HEM200 3.0 67.4 1.0 CD2 A:HIS94 3.1 67.5 1.0 C1D A:HEM200 3.1 66.3 1.0 C1B A:HEM200 3.1 65.6 1.0 C4B A:HEM200 3.1 67.0 1.0 C4A A:HEM200 3.1 64.2 1.0 C4D A:HEM200 3.1 66.4 1.0 C1A A:HEM200 3.1 65.4 1.0 CE1 A:HIS94 3.2 64.5 1.0 CHD A:HEM200 3.4 65.1 1.0 CHC A:HEM200 3.4 66.3 1.0 CHB A:HEM200 3.4 63.4 1.0 CHA A:HEM200 3.5 66.0 1.0 C2C A:HEM200 4.2 66.6 1.0 C3C A:HEM200 4.2 66.2 1.0 CG A:HIS94 4.2 68.0 1.0 ND1 A:HIS94 4.3 67.0 1.0 C2D A:HEM200 4.3 67.7 1.0 C2B A:HEM200 4.3 64.4 1.0 C3B A:HEM200 4.3 64.1 1.0 C3D A:HEM200 4.3 64.9 1.0 C3A A:HEM200 4.3 62.8 1.0 C2A A:HEM200 4.3 65.8 1.0 CG2 A:VAL66 4.4 59.9 1.0 CG1 A:VAL66 4.6 60.2 1.0 NH1 A:ARG97 4.7 69.7 1.0

Iron binding site 2 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% 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 58% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:53.2 occ:1.00 FE B:HEM200 0.0 53.2 1.0 O1 B:OXY201 1.8 56.2 0.6 NC B:HEM200 2.0 55.7 1.0 NB B:HEM200 2.0 52.2 1.0 ND B:HEM200 2.1 55.5 1.0 NA B:HEM200 2.1 53.8 1.0 NE2 B:HIS94 2.2 61.1 1.0 O2 B:OXY201 2.9 56.2 0.6 CD2 B:HIS94 3.0 59.7 1.0 C1C B:HEM200 3.0 55.3 1.0 C4C B:HEM200 3.0 56.5 1.0 C4B B:HEM200 3.0 53.7 1.0 C1B B:HEM200 3.1 52.7 1.0 C1D B:HEM200 3.1 58.5 1.0 C4A B:HEM200 3.1 54.6 1.0 C4D B:HEM200 3.1 55.9 1.0 C1A B:HEM200 3.1 56.2 1.0 CE1 B:HIS94 3.2 62.5 1.0 CHC B:HEM200 3.4 55.0 1.0 CHD B:HEM200 3.4 56.1 1.0 CHB B:HEM200 3.4 52.3 1.0 CHA B:HEM200 3.5 57.2 1.0 CG B:HIS94 4.2 61.5 1.0 ND1 B:HIS94 4.3 63.3 1.0 C2C B:HEM200 4.3 52.0 1.0 C3C B:HEM200 4.3 54.7 1.0 C2B B:HEM200 4.3 51.1 1.0 C3B B:HEM200 4.3 51.0 1.0 C2D B:HEM200 4.3 60.3 1.0 C3D B:HEM200 4.3 60.7 1.0 C3A B:HEM200 4.3 54.2 1.0 CG2 B:VAL66 4.3 53.8 1.0 C2A B:HEM200 4.3 55.1 1.0 CG1 B:VAL66 4.7 50.6 1.0

Iron binding site 3 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% 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 58% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:67.4 occ:1.00 FE C:HEM200 0.0 67.4 1.0 O1 C:OXY201 1.8 71.5 0.7 ND C:HEM200 2.1 74.1 1.0 NA C:HEM200 2.1 71.2 1.0 NB C:HEM200 2.1 72.0 1.0 NC C:HEM200 2.1 72.6 1.0 NE2 C:HIS98 2.2 66.7 1.0 O2 C:OXY201 2.9 71.8 0.7 C4A C:HEM200 3.0 71.4 1.0 C1B C:HEM200 3.1 70.6 1.0 C4C C:HEM200 3.1 71.8 1.0 C4D C:HEM200 3.1 72.5 1.0 C1D C:HEM200 3.1 74.8 1.0 C1A C:HEM200 3.1 75.0 1.0 C4B C:HEM200 3.1 70.4 1.0 C1C C:HEM200 3.1 73.0 1.0 CE1 C:HIS98 3.1 67.7 1.0 CD2 C:HIS98 3.1 66.0 1.0 CHB C:HEM200 3.4 72.5 1.0 CHD C:HEM200 3.4 74.4 1.0 CHA C:HEM200 3.4 72.7 1.0 CHC C:HEM200 3.5 70.7 1.0 ND1 C:HIS98 4.2 67.3 1.0 C3A C:HEM200 4.3 71.5 1.0 CG C:HIS98 4.3 67.1 1.0 C2B C:HEM200 4.3 67.2 1.0 C2D C:HEM200 4.3 72.4 1.0 C3D C:HEM200 4.3 73.3 1.0 C3C C:HEM200 4.3 73.0 1.0 C2A C:HEM200 4.3 71.4 1.0 C3B C:HEM200 4.3 69.7 1.0 C2C C:HEM200 4.3 73.7 1.0 CG1 C:VAL70 4.5 62.8 1.0 CG2 C:VAL70 4.5 66.3 1.0 NH2 C:ARG101 4.7 69.6 1.0

Iron binding site 4 out of 4 in the Oxy-Deoxy Intermediate of 400 kDa Giant Hemoglobin at 58% 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 58% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe200 b:67.7 occ:1.00 FE D:HEM200 0.0 67.7 1.0 O1 D:OXY201 1.8 65.5 0.3 NB D:HEM200 2.1 63.2 1.0 NC D:HEM200 2.1 68.1 1.0 NA D:HEM200 2.1 66.3 1.0 ND D:HEM200 2.1 67.1 1.0 NE2 D:HIS96 2.2 66.7 1.0 O2 D:OXY201 2.8 66.8 0.3 C4B D:HEM200 3.1 59.4 1.0 C1C D:HEM200 3.1 65.6 1.0 C1B D:HEM200 3.1 64.7 1.0 C4A D:HEM200 3.1 63.5 1.0 C4C D:HEM200 3.1 68.0 1.0 C1A D:HEM200 3.1 66.1 1.0 C1D D:HEM200 3.1 68.2 1.0 C4D D:HEM200 3.1 67.6 1.0 CD2 D:HIS96 3.1 70.1 1.0 CE1 D:HIS96 3.1 66.0 1.0 CHC D:HEM200 3.4 61.6 1.0 CHB D:HEM200 3.4 63.4 1.0 CHD D:HEM200 3.5 68.7 1.0 CHA D:HEM200 3.5 65.7 1.0 ND1 D:HIS96 4.2 67.7 1.0 C3B D:HEM200 4.3 58.2 1.0 CG D:HIS96 4.3 69.0 1.0 C2B D:HEM200 4.3 61.5 1.0 C2C D:HEM200 4.3 66.6 1.0 C3C D:HEM200 4.3 69.4 1.0 C3A D:HEM200 4.3 61.3 1.0 C2A D:HEM200 4.3 63.2 1.0 C2D D:HEM200 4.3 68.4 1.0 C3D D:HEM200 4.3 70.4 1.0 CG2 D:VAL68 4.6 61.5 1.0 CG1 D:VAL68 4.6 57.8 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