Iron in PDB 7vld: Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation, PDB code: 7vld was solved by N.Numoto, S.Onoda, 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)	49.24 / 2.10
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	110.263, 110.263, 196.968, 90, 90, 120
R / Rfree (%)	19 / 22.1

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation (pdb code 7vld). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation, PDB code: 7vld:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in the Oxy-Deoxy Intermediate of V2 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 V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:29.1 occ:1.00 FE A:HEM200 0.0 29.1 1.0 O1 A:OXY201 1.8 30.6 0.5 NC A:HEM200 2.0 30.6 1.0 ND A:HEM200 2.0 30.5 1.0 NA A:HEM200 2.1 30.7 1.0 NE2 A:HIS94 2.1 30.4 1.0 NB A:HEM200 2.1 36.0 1.0 O2 A:OXY201 2.8 31.6 0.5 CE1 A:HIS94 3.1 30.9 1.0 C4C A:HEM200 3.1 32.6 1.0 C1D A:HEM200 3.1 34.1 1.0 CD2 A:HIS94 3.1 29.3 1.0 C4D A:HEM200 3.1 34.8 1.0 C1C A:HEM200 3.1 34.9 1.0 C4B A:HEM200 3.1 31.5 1.0 C1B A:HEM200 3.1 29.3 1.0 C4A A:HEM200 3.1 29.6 1.0 C1A A:HEM200 3.1 28.4 1.0 CHD A:HEM200 3.4 31.8 1.0 CHC A:HEM200 3.5 32.9 1.0 CHA A:HEM200 3.5 32.2 1.0 CHB A:HEM200 3.5 28.2 1.0 ND1 A:HIS94 4.2 24.3 1.0 CG A:HIS94 4.2 29.5 1.0 C2D A:HEM200 4.3 29.6 1.0 C3C A:HEM200 4.3 33.1 1.0 C3D A:HEM200 4.3 34.4 1.0 C2C A:HEM200 4.3 33.9 1.0 C2B A:HEM200 4.3 33.9 1.0 C3B A:HEM200 4.3 30.1 1.0 C3A A:HEM200 4.3 31.2 1.0 C2A A:HEM200 4.3 32.4 1.0 NH1 A:ARG97 4.5 29.6 0.5 CG2 A:VAL66 4.6 32.2 1.0 O A:HOH325 4.8 37.4 1.0 CE1 A:HIS62 4.9 31.9 1.0

Iron binding site 2 out of 8 in the Oxy-Deoxy Intermediate of V2 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 V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:35.5 occ:1.00 FE B:HEM201 0.0 35.5 1.0 O1 B:OXY202 1.8 36.2 0.7 NC B:HEM201 2.0 32.8 1.0 ND B:HEM201 2.0 35.3 1.0 NB B:HEM201 2.1 31.1 1.0 NA B:HEM201 2.1 35.5 1.0 NE2 B:HIS95 2.1 35.1 1.0 O2 B:OXY202 2.8 33.6 0.7 CD2 B:HIS95 3.0 31.4 1.0 C4C B:HEM201 3.0 34.0 1.0 C1C B:HEM201 3.0 33.6 1.0 C1D B:HEM201 3.1 38.2 1.0 C1B B:HEM201 3.1 30.3 1.0 C4D B:HEM201 3.1 36.1 1.0 C4A B:HEM201 3.1 32.9 1.0 C4B B:HEM201 3.1 30.6 1.0 C1A B:HEM201 3.1 34.9 1.0 CE1 B:HIS95 3.1 38.0 1.0 CHC B:HEM201 3.4 33.8 1.0 CHD B:HEM201 3.4 34.9 1.0 CHB B:HEM201 3.4 27.2 1.0 CHA B:HEM201 3.5 33.2 1.0 CG B:HIS95 4.2 43.4 1.0 ND1 B:HIS95 4.2 36.5 1.0 C2C B:HEM201 4.3 32.9 1.0 C3C B:HEM201 4.3 34.8 1.0 C3D B:HEM201 4.3 35.5 1.0 C2D B:HEM201 4.3 40.6 1.0 C2B B:HEM201 4.3 32.2 1.0 C3A B:HEM201 4.3 34.4 1.0 C3B B:HEM201 4.3 27.9 1.0 C2A B:HEM201 4.3 33.2 1.0 CG2 B:VAL67 4.6 28.0 1.0 CE1 B:HIS63 4.8 38.5 1.0

Iron binding site 3 out of 8 in the Oxy-Deoxy Intermediate of V2 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 V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:37.2 occ:1.00 FE C:HEM200 0.0 37.2 1.0 O1 C:OXY201 1.8 36.9 0.9 NB C:HEM200 2.0 37.2 1.0 NC C:HEM200 2.0 36.1 1.0 NA C:HEM200 2.1 36.4 1.0 ND C:HEM200 2.1 40.1 1.0 NE2 C:HIS99 2.1 33.9 1.0 CD2 C:HIS99 2.8 39.1 1.0 O2 C:OXY201 2.8 39.2 0.9 C1B C:HEM200 3.0 35.0 1.0 C4A C:HEM200 3.1 38.4 1.0 C4C C:HEM200 3.1 42.0 1.0 C1D C:HEM200 3.1 38.5 1.0 C4B C:HEM200 3.1 37.1 1.0 C1C C:HEM200 3.1 38.6 1.0 C4D C:HEM200 3.1 37.3 1.0 C1A C:HEM200 3.1 40.3 1.0 CE1 C:HIS99 3.2 40.5 1.0 CHB C:HEM200 3.4 34.8 1.0 CHD C:HEM200 3.4 36.4 1.0 CHC C:HEM200 3.4 38.8 1.0 CHA C:HEM200 3.5 41.0 1.0 CG C:HIS99 4.0 39.8 1.0 ND1 C:HIS99 4.2 36.1 1.0 C2B C:HEM200 4.3 40.2 1.0 C3B C:HEM200 4.3 39.5 1.0 C3A C:HEM200 4.3 37.8 1.0 C3C C:HEM200 4.3 43.5 1.0 C2C C:HEM200 4.3 35.8 1.0 C2D C:HEM200 4.3 49.5 1.0 C3D C:HEM200 4.3 43.6 1.0 C2A C:HEM200 4.3 37.3 1.0 CG2 C:VAL71 4.5 36.7 1.0 CE1 C:HIS67 4.8 35.3 1.0

Iron binding site 4 out of 8 in the Oxy-Deoxy Intermediate of V2 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 V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:36.0 occ:1.00 FE D:HEM201 0.0 36.0 1.0 O1 D:OXY202 1.8 34.5 0.6 ND D:HEM201 2.0 40.7 1.0 NA D:HEM201 2.1 36.9 1.0 NE2 D:HIS99 2.1 33.1 1.0 NB D:HEM201 2.1 29.4 1.0 NC D:HEM201 2.1 36.2 1.0 O2 D:OXY202 2.8 37.0 0.6 CD2 D:HIS99 3.0 34.4 1.0 C1D D:HEM201 3.1 43.6 1.0 CE1 D:HIS99 3.1 37.2 1.0 C4D D:HEM201 3.1 40.7 1.0 C4A D:HEM201 3.1 37.3 1.0 C1B D:HEM201 3.1 32.2 1.0 C1A D:HEM201 3.1 37.4 1.0 C4C D:HEM201 3.1 37.9 1.0 C1C D:HEM201 3.1 37.0 1.0 C4B D:HEM201 3.1 36.6 1.0 CHD D:HEM201 3.4 38.3 1.0 CHB D:HEM201 3.4 31.8 1.0 CHA D:HEM201 3.4 35.1 1.0 CHC D:HEM201 3.5 32.7 1.0 ND1 D:HIS99 4.2 32.7 1.0 CG D:HIS99 4.2 40.0 1.0 C2D D:HEM201 4.3 41.6 1.0 C3D D:HEM201 4.3 42.1 1.0 C3A D:HEM201 4.3 36.9 1.0 C2A D:HEM201 4.3 39.1 1.0 C2C D:HEM201 4.3 36.7 1.0 C2B D:HEM201 4.3 33.1 1.0 C3C D:HEM201 4.3 41.6 1.0 C3B D:HEM201 4.3 34.6 1.0 O D:HOH348 4.6 41.3 1.0 CG2 D:VAL71 4.6 29.1 1.0 CZ D:PHE110 4.9 37.6 1.0

Iron binding site 5 out of 8 in the Oxy-Deoxy Intermediate of V2 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 5 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ E:Fe200 b:31.0 occ:1.00 FE E:HEM200 0.0 31.0 1.0 O1 E:OXY201 1.8 32.5 0.8 NA E:HEM200 2.0 32.2 1.0 NC E:HEM200 2.1 33.5 1.0 ND E:HEM200 2.1 35.4 1.0 NE2 E:HIS94 2.1 27.9 1.0 NB E:HEM200 2.1 28.7 1.0 O2 E:OXY201 2.8 35.1 0.8 CE1 E:HIS94 3.0 31.8 1.0 C4C E:HEM200 3.0 35.0 1.0 C4A E:HEM200 3.1 33.7 1.0 C1D E:HEM200 3.1 35.7 1.0 C1B E:HEM200 3.1 28.3 1.0 CD2 E:HIS94 3.1 29.8 1.0 C1A E:HEM200 3.1 29.1 1.0 C4D E:HEM200 3.1 32.8 1.0 C1C E:HEM200 3.1 32.8 1.0 C4B E:HEM200 3.1 31.0 1.0 CHD E:HEM200 3.4 29.6 1.0 CHB E:HEM200 3.4 31.1 1.0 CHA E:HEM200 3.5 29.0 1.0 CHC E:HEM200 3.5 30.4 1.0 ND1 E:HIS94 4.2 29.4 1.0 CG E:HIS94 4.2 33.0 1.0 C3A E:HEM200 4.3 29.7 1.0 C3C E:HEM200 4.3 34.9 1.0 C2D E:HEM200 4.3 35.9 1.0 C2A E:HEM200 4.3 31.1 1.0 C2B E:HEM200 4.3 31.9 1.0 C3D E:HEM200 4.3 34.3 1.0 C2C E:HEM200 4.3 37.3 1.0 C3B E:HEM200 4.3 31.3 1.0 O E:HOH352 4.5 40.7 1.0 CG2 E:VAL66 4.7 29.2 1.0 CE1 E:HIS62 4.9 31.3 1.0

Iron binding site 6 out of 8 in the Oxy-Deoxy Intermediate of V2 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 6 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:36.0 occ:1.00 FE F:HEM201 0.0 36.0 1.0 O1 F:OXY202 1.8 33.6 0.8 NB F:HEM201 2.0 31.0 1.0 NC F:HEM201 2.0 32.8 1.0 NA F:HEM201 2.0 31.1 1.0 ND F:HEM201 2.1 30.1 1.0 NE2 F:HIS95 2.1 33.7 1.0 O2 F:OXY202 2.8 33.2 0.8 CD2 F:HIS95 3.0 33.2 1.0 C4B F:HEM201 3.1 31.7 1.0 C1C F:HEM201 3.1 35.5 1.0 C1B F:HEM201 3.1 26.7 1.0 C4C F:HEM201 3.1 35.7 1.0 C4A F:HEM201 3.1 29.9 1.0 C1A F:HEM201 3.1 32.9 1.0 C4D F:HEM201 3.1 31.7 1.0 C1D F:HEM201 3.1 30.1 1.0 CE1 F:HIS95 3.1 36.6 1.0 CHC F:HEM201 3.4 35.5 1.0 CHB F:HEM201 3.4 26.3 1.0 CHA F:HEM201 3.4 33.2 1.0 CHD F:HEM201 3.4 32.5 1.0 CG F:HIS95 4.2 45.9 1.0 ND1 F:HIS95 4.2 34.7 1.0 C3B F:HEM201 4.3 28.2 1.0 C2B F:HEM201 4.3 31.4 1.0 C2C F:HEM201 4.3 31.7 1.0 C3C F:HEM201 4.3 35.1 1.0 C3A F:HEM201 4.3 28.1 1.0 C2A F:HEM201 4.3 27.2 1.0 C3D F:HEM201 4.3 32.1 1.0 C2D F:HEM201 4.3 32.4 1.0 CG2 F:VAL67 4.7 27.0 1.0 CE1 F:HIS63 4.8 28.9 1.0

Iron binding site 7 out of 8 in the Oxy-Deoxy Intermediate of V2 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 7 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ G:Fe200 b:38.8 occ:1.00 FE G:HEM200 0.0 38.8 1.0 O1 G:OXY201 1.8 38.1 0.8 ND G:HEM200 2.0 38.4 1.0 NC G:HEM200 2.0 43.0 1.0 NB G:HEM200 2.0 38.7 1.0 NA G:HEM200 2.1 39.6 1.0 NE2 G:HIS99 2.1 37.0 1.0 O2 G:OXY201 2.8 38.5 0.8 CD2 G:HIS99 2.9 41.3 1.0 C1D G:HEM200 3.1 40.9 1.0 C1B G:HEM200 3.1 32.4 1.0 C4C G:HEM200 3.1 40.2 1.0 C4A G:HEM200 3.1 33.2 1.0 C1C G:HEM200 3.1 41.4 1.0 C4D G:HEM200 3.1 38.3 1.0 C4B G:HEM200 3.1 39.4 1.0 C1A G:HEM200 3.1 38.6 1.0 CE1 G:HIS99 3.1 39.8 1.0 CHD G:HEM200 3.4 38.8 1.0 CHB G:HEM200 3.4 31.7 1.0 CHC G:HEM200 3.4 34.8 1.0 CHA G:HEM200 3.5 38.4 1.0 CG G:HIS99 4.1 46.5 1.0 ND1 G:HIS99 4.2 40.6 1.0 C2D G:HEM200 4.3 40.9 1.0 C3A G:HEM200 4.3 35.6 1.0 C2B G:HEM200 4.3 37.5 1.0 C3D G:HEM200 4.3 37.4 1.0 C3C G:HEM200 4.3 37.8 1.0 C2C G:HEM200 4.3 41.1 1.0 C2A G:HEM200 4.3 35.7 1.0 C3B G:HEM200 4.3 37.4 1.0 CG2 G:VAL71 4.7 31.0 1.0 CE1 G:HIS67 4.7 31.2 1.0

Iron binding site 8 out of 8 in the Oxy-Deoxy Intermediate of V2 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 8 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 69% Oxygen Saturation within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:29.2 occ:1.00 FE H:HEM201 0.0 29.2 1.0 O1 H:OXY202 1.8 31.1 0.4 NC H:HEM201 2.0 31.8 1.0 ND H:HEM201 2.0 35.7 1.0 NE2 H:HIS99 2.1 31.5 1.0 NA H:HEM201 2.1 30.6 1.0 NB H:HEM201 2.1 27.1 1.0 O2 H:OXY202 2.8 31.5 0.4 CE1 H:HIS99 3.0 32.9 1.0 C4C H:HEM201 3.0 32.0 1.0 C1D H:HEM201 3.0 33.6 1.0 C1C H:HEM201 3.1 35.2 1.0 C4D H:HEM201 3.1 33.2 1.0 C1B H:HEM201 3.1 27.3 1.0 C4A H:HEM201 3.1 28.8 1.0 C1A H:HEM201 3.1 31.4 1.0 CD2 H:HIS99 3.1 34.4 1.0 C4B H:HEM201 3.1 28.8 1.0 CHD H:HEM201 3.4 31.6 1.0 CHB H:HEM201 3.4 28.0 1.0 CHC H:HEM201 3.5 31.7 1.0 CHA H:HEM201 3.5 34.5 1.0 ND1 H:HIS99 4.1 32.8 1.0 CG H:HIS99 4.2 34.8 1.0 C3C H:HEM201 4.3 34.6 1.0 C2D H:HEM201 4.3 33.6 1.0 C2C H:HEM201 4.3 30.9 1.0 C3D H:HEM201 4.3 36.7 1.0 C2B H:HEM201 4.3 28.8 1.0 C3A H:HEM201 4.3 31.5 1.0 C2A H:HEM201 4.3 36.1 1.0 C3B H:HEM201 4.3 29.1 1.0 CG2 H:VAL71 4.6 24.8 1.0 CE1 H:HIS67 4.9 31.1 1.0 CZ H:PHE110 5.0 36.2 1.0

N.Numoto, S.Onoda, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito. Structures of Oxygen Dissociation Intermediates of 400 kDa V2 Hemoglobin Provide Coarse Snapshots of the Protein Allostery. Biophys Physicobio. V. 19 1 2022.
ISSN: ESSN 2189-4779
PubMed: 35797404
DOI: 10.2142/BIOPHYSICO.BPPB-V19.0019