Iron in PDB 6kai: Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light

The structure of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light, PDB code: 6kai was solved by N.Shibayama, S.Y.Park, M.Ohki, A.Sato-Tomita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.589, 94.415, 99.956, 90.00, 101.97, 90.00
R / Rfree (%)	17.5 / 20.2

The structure of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light also contains other interesting chemical elements:

Nickel

(Ni)

4 atoms

The binding sites of Iron atom in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light (pdb code 6kai). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light, PDB code: 6kai:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:8.8 occ:1.00 FE B:HEM201 0.0 8.8 1.0 ND B:HEM201 2.0 11.5 1.0 NA B:HEM201 2.1 7.4 1.0 NB B:HEM201 2.1 9.6 1.0 NC B:HEM201 2.1 8.3 1.0 NE2 B:HIS92 2.2 10.0 1.0 C4D B:HEM201 3.0 7.4 1.0 C1A B:HEM201 3.1 10.8 1.0 C4B B:HEM201 3.1 7.7 1.0 C1D B:HEM201 3.1 10.5 1.0 C1C B:HEM201 3.1 7.7 1.0 C4C B:HEM201 3.1 8.2 1.0 C1B B:HEM201 3.1 9.7 1.0 C4A B:HEM201 3.1 9.4 1.0 CE1 B:HIS92 3.1 11.2 1.0 CD2 B:HIS92 3.3 8.0 1.0 CHA B:HEM201 3.4 9.8 1.0 CHC B:HEM201 3.4 9.7 1.0 CHD B:HEM201 3.4 9.3 1.0 CHB B:HEM201 3.5 9.1 1.0 CG2 B:VAL67 4.1 14.2 1.0 NE2 B:HIS63 4.2 25.4 1.0 C3D B:HEM201 4.3 9.1 1.0 C2D B:HEM201 4.3 9.4 1.0 C3B B:HEM201 4.3 10.3 1.0 C2A B:HEM201 4.3 10.7 1.0 ND1 B:HIS92 4.3 10.1 1.0 C2B B:HEM201 4.3 9.5 1.0 C2C B:HEM201 4.3 9.7 1.0 C3C B:HEM201 4.3 9.2 1.0 C3A B:HEM201 4.3 9.5 1.0 CG B:HIS92 4.4 7.4 1.0 CE1 B:HIS63 4.8 11.4 1.0 CD1 B:LEU96 4.8 10.9 1.0

Iron binding site 2 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:14.7 occ:1.00 FE D:HEM201 0.0 14.7 1.0 ND D:HEM201 2.0 14.7 1.0 NA D:HEM201 2.1 14.6 1.0 NB D:HEM201 2.1 13.8 1.0 NC D:HEM201 2.1 14.5 1.0 NE2 D:HIS92 2.3 16.0 1.0 C1B D:HEM201 3.1 15.8 1.0 C1D D:HEM201 3.1 16.9 1.0 C4A D:HEM201 3.1 17.9 1.0 C1A D:HEM201 3.1 18.0 1.0 C4D D:HEM201 3.1 18.7 1.0 C4C D:HEM201 3.1 15.5 1.0 C4B D:HEM201 3.1 14.5 1.0 C1C D:HEM201 3.1 15.9 1.0 CE1 D:HIS92 3.2 16.9 1.0 CD2 D:HIS92 3.3 12.4 1.0 CHB D:HEM201 3.4 13.8 1.0 CHD D:HEM201 3.4 16.8 1.0 CHA D:HEM201 3.5 15.6 1.0 CHC D:HEM201 3.5 15.1 1.0 CG2 D:VAL67 4.2 15.6 1.0 NE2 D:HIS63 4.2 28.9 1.0 C2D D:HEM201 4.3 18.3 1.0 C3A D:HEM201 4.3 18.1 1.0 C2B D:HEM201 4.3 14.6 1.0 C2A D:HEM201 4.3 15.5 1.0 C3D D:HEM201 4.3 15.6 1.0 C3B D:HEM201 4.3 15.0 1.0 C3C D:HEM201 4.3 16.7 1.0 C2C D:HEM201 4.3 17.9 1.0 ND1 D:HIS92 4.4 16.3 1.0 CG D:HIS92 4.4 13.9 1.0 CE1 D:HIS63 4.7 22.0 1.0 CD1 D:LEU96 4.9 16.7 1.0

Iron binding site 3 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light within 5.0Å range: probe atom residue distance (Å) B Occ F:Fe201 b:11.1 occ:1.00 FE F:HEM201 0.0 11.1 1.0 ND F:HEM201 2.1 8.5 1.0 NB F:HEM201 2.1 8.7 1.0 NC F:HEM201 2.1 11.6 1.0 NA F:HEM201 2.1 12.1 1.0 NE2 F:HIS92 2.2 10.2 1.0 C4B F:HEM201 3.1 8.7 1.0 C4D F:HEM201 3.1 11.4 1.0 C1C F:HEM201 3.1 9.8 1.0 C1D F:HEM201 3.1 10.3 1.0 CE1 F:HIS92 3.1 11.3 1.0 C1B F:HEM201 3.1 11.7 1.0 C1A F:HEM201 3.1 11.6 1.0 C4C F:HEM201 3.1 9.5 1.0 C4A F:HEM201 3.1 11.7 1.0 CD2 F:HIS92 3.3 8.2 1.0 CHC F:HEM201 3.4 10.4 1.0 CHA F:HEM201 3.4 12.3 1.0 CHD F:HEM201 3.5 10.3 1.0 CHB F:HEM201 3.5 12.3 1.0 CG2 F:VAL67 4.0 13.3 1.0 NE2 F:HIS63 4.2 18.9 1.0 ND1 F:HIS92 4.3 10.3 1.0 C3D F:HEM201 4.3 12.2 1.0 C3B F:HEM201 4.3 9.5 1.0 C2D F:HEM201 4.3 10.2 1.0 C2B F:HEM201 4.3 12.9 1.0 C2C F:HEM201 4.3 10.9 1.0 C2A F:HEM201 4.3 12.1 1.0 C3A F:HEM201 4.3 12.7 1.0 C3C F:HEM201 4.3 11.2 1.0 CG F:HIS92 4.4 8.4 1.0 CE1 F:HIS63 4.8 13.7 1.0 CD1 F:LEU96 4.9 14.1 1.0

Iron binding site 4 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Closslinked Alpha(Ni)-Beta(Fe) Human Hemoglobin A in the T Quaternary Structure at 95 K: Light within 5.0Å range: probe atom residue distance (Å) B Occ H:Fe201 b:13.2 occ:1.00 FE H:HEM201 0.0 13.2 1.0 NB H:HEM201 2.0 13.2 1.0 ND H:HEM201 2.0 11.9 1.0 NA H:HEM201 2.1 14.6 1.0 NC H:HEM201 2.1 12.2 1.0 NE2 H:HIS92 2.3 12.2 1.0 C4B H:HEM201 3.1 9.9 1.0 C1D H:HEM201 3.1 12.1 1.0 C1B H:HEM201 3.1 11.8 1.0 C4A H:HEM201 3.1 13.4 1.0 C4D H:HEM201 3.1 13.2 1.0 C4C H:HEM201 3.1 9.7 1.0 C1C H:HEM201 3.1 11.3 1.0 C1A H:HEM201 3.1 13.1 1.0 CE1 H:HIS92 3.1 14.9 1.0 CD2 H:HIS92 3.3 12.2 1.0 CHD H:HEM201 3.4 12.7 1.0 CHB H:HEM201 3.4 17.2 1.0 CHC H:HEM201 3.4 15.0 1.0 CHA H:HEM201 3.5 14.1 1.0 CG2 H:VAL67 4.2 14.3 1.0 NE2 H:HIS63 4.2 24.9 1.0 C2D H:HEM201 4.3 16.3 1.0 C3B H:HEM201 4.3 11.7 1.0 C2B H:HEM201 4.3 14.0 1.0 C3D H:HEM201 4.3 12.5 1.0 C3A H:HEM201 4.3 15.3 1.0 ND1 H:HIS92 4.3 14.0 1.0 C2A H:HEM201 4.3 14.5 1.0 C3C H:HEM201 4.3 13.2 1.0 C2C H:HEM201 4.3 10.7 1.0 CG H:HIS92 4.4 12.8 1.0 CE1 H:HIS63 4.7 17.9 1.0 CD1 H:LEU96 4.9 19.1 1.0

N.Shibayama, A.Sato-Tomita, M.Ohki, K.Ichiyanagi, S.Y.Park. Direct Observation of Ligand Migration Within Human Hemoglobin at Work Proc.Natl.Acad.Sci.Usa 2020.
ISSN: ESSN 1091-6490