Nickel in PDB 6ka9: Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark

The structure of Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6ka9 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)	19.83 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.639, 94.189, 100.317, 90.00, 101.63, 90.00
R / Rfree (%)	16.6 / 19.1

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

Iron

(Fe)

4 atoms

The binding sites of Nickel atom in the Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark (pdb code 6ka9). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 4 binding sites of Nickel where determined in the Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6ka9:
Jump to Nickel binding site number: 1; 2; 3; 4;

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni201 b:5.7 occ:1.00 NI B:HNI201 0.0 5.7 1.0 NB B:HNI201 2.0 8.3 1.0 NA B:HNI201 2.1 7.0 1.0 NC B:HNI201 2.1 5.3 1.0 ND B:HNI201 2.1 8.3 1.0 NE2 B:HIS92 2.2 6.3 1.0 C4B B:HNI201 3.0 6.5 1.0 C1C B:HNI201 3.1 5.8 1.0 C1A B:HNI201 3.1 5.9 1.0 C4D B:HNI201 3.1 6.3 1.0 C1B B:HNI201 3.1 7.2 1.0 C4A B:HNI201 3.1 7.0 1.0 C4C B:HNI201 3.1 6.2 1.0 CE1 B:HIS92 3.1 8.3 1.0 C1D B:HNI201 3.1 7.0 1.0 CD2 B:HIS92 3.2 6.0 1.0 CHC B:HNI201 3.4 6.4 1.0 CHA B:HNI201 3.4 5.7 1.0 CHB B:HNI201 3.4 6.4 1.0 CHD B:HNI201 3.5 6.8 1.0 CG2 B:VAL67 3.9 10.4 1.0 NE2 B:HIS63 4.1 9.4 1.0 ND1 B:HIS92 4.2 7.0 1.0 C3B B:HNI201 4.3 5.7 1.0 C2B B:HNI201 4.3 7.4 1.0 C2C B:HNI201 4.3 4.9 1.0 C2A B:HNI201 4.3 5.7 1.0 C3C B:HNI201 4.3 7.0 1.0 C3A B:HNI201 4.3 6.9 1.0 C3D B:HNI201 4.3 7.5 1.0 C2D B:HNI201 4.3 6.6 1.0 CG B:HIS92 4.3 6.0 1.0 CE1 B:HIS63 4.8 13.6 1.0 CD1 B:LEU96 5.0 9.6 1.0 CE1 B:PHE103 5.0 8.9 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ D:Ni202 b:9.6 occ:1.00 NI D:HNI202 0.0 9.6 1.0 ND D:HNI202 2.0 11.7 1.0 NA D:HNI202 2.1 12.7 1.0 NC D:HNI202 2.1 11.0 1.0 NB D:HNI202 2.1 10.5 1.0 NE2 D:HIS92 2.2 10.2 1.0 C1D D:HNI202 3.0 13.9 1.0 C4C D:HNI202 3.0 11.3 1.0 C4D D:HNI202 3.0 13.2 1.0 C4B D:HNI202 3.1 9.8 1.0 C1A D:HNI202 3.1 11.3 1.0 C1C D:HNI202 3.1 9.4 1.0 C1B D:HNI202 3.1 10.2 1.0 C4A D:HNI202 3.1 13.3 1.0 CE1 D:HIS92 3.2 11.4 1.0 CD2 D:HIS92 3.2 9.6 1.0 CHD D:HNI202 3.4 11.1 1.0 CHC D:HNI202 3.4 9.6 1.0 CHA D:HNI202 3.4 12.6 1.0 CHB D:HNI202 3.5 12.7 1.0 CG2 D:VAL67 4.0 10.5 1.0 NE2 D:HIS63 4.2 19.1 1.0 C3C D:HNI202 4.2 13.2 1.0 C2C D:HNI202 4.3 11.4 1.0 C2D D:HNI202 4.3 13.0 1.0 C3D D:HNI202 4.3 13.4 1.0 C2A D:HNI202 4.3 14.2 1.0 C3A D:HNI202 4.3 11.4 1.0 ND1 D:HIS92 4.3 9.3 1.0 C2B D:HNI202 4.3 11.2 1.0 C3B D:HNI202 4.4 10.6 1.0 CE1 D:HIS63 4.4 25.9 1.0 CG D:HIS92 4.4 9.3 1.0 CD1 D:LEU96 4.9 12.8 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ F:Ni201 b:5.8 occ:1.00 NI F:HNI201 0.0 5.8 1.0 NC F:HNI201 2.0 7.4 1.0 NA F:HNI201 2.0 8.0 1.0 NB F:HNI201 2.1 7.1 1.0 ND F:HNI201 2.1 7.5 1.0 NE2 F:HIS92 2.2 5.7 1.0 C1C F:HNI201 3.1 7.5 1.0 C4C F:HNI201 3.1 5.4 1.0 C4B F:HNI201 3.1 6.3 1.0 C4A F:HNI201 3.1 6.6 1.0 C1A F:HNI201 3.1 7.4 1.0 C4D F:HNI201 3.1 6.5 1.0 C1B F:HNI201 3.1 7.8 1.0 C1D F:HNI201 3.1 7.0 1.0 CE1 F:HIS92 3.1 7.8 1.0 CD2 F:HIS92 3.2 5.9 1.0 CHC F:HNI201 3.4 7.2 1.0 CHA F:HNI201 3.4 7.3 1.0 CHD F:HNI201 3.4 5.8 1.0 CHB F:HNI201 3.4 8.5 1.0 CG2 F:VAL67 3.9 9.5 1.0 NE2 F:HIS63 4.1 11.3 1.0 ND1 F:HIS92 4.2 6.9 1.0 C3C F:HNI201 4.3 6.3 1.0 C2A F:HNI201 4.3 7.8 1.0 C2C F:HNI201 4.3 7.5 1.0 C3A F:HNI201 4.3 8.0 1.0 C3B F:HNI201 4.3 6.0 1.0 C3D F:HNI201 4.3 8.1 1.0 C2D F:HNI201 4.3 8.7 1.0 C2B F:HNI201 4.3 8.0 1.0 CG F:HIS92 4.3 6.3 1.0 CE1 F:HIS63 4.6 12.8 1.0 CD1 F:LEU96 5.0 8.2 1.0

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Closslinked Alpha(Fe-Co)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ H:Ni201 b:8.0 occ:1.00 NI H:HNI201 0.0 8.0 1.0 ND H:HNI201 2.0 10.4 1.0 NC H:HNI201 2.0 8.4 1.0 NA H:HNI201 2.1 10.3 1.0 NB H:HNI201 2.1 9.6 1.0 NE2 H:HIS92 2.2 8.8 1.0 C4C H:HNI201 3.0 7.8 1.0 C1D H:HNI201 3.1 7.8 1.0 C4D H:HNI201 3.1 9.3 1.0 C1A H:HNI201 3.1 9.4 1.0 C4A H:HNI201 3.1 9.8 1.0 C1C H:HNI201 3.1 7.8 1.0 C1B H:HNI201 3.1 8.8 1.0 C4B H:HNI201 3.1 8.3 1.0 CE1 H:HIS92 3.1 11.9 1.0 CD2 H:HIS92 3.3 7.5 1.0 CHD H:HNI201 3.4 8.9 1.0 CHB H:HNI201 3.4 9.8 1.0 CHA H:HNI201 3.4 9.8 1.0 CHC H:HNI201 3.5 9.1 1.0 CG2 H:VAL67 4.0 10.2 1.0 NE2 H:HIS63 4.0 12.6 1.0 ND1 H:HIS92 4.3 10.6 1.0 C3D H:HNI201 4.3 10.4 1.0 C2D H:HNI201 4.3 10.8 1.0 C3C H:HNI201 4.3 8.2 1.0 C2C H:HNI201 4.3 7.7 1.0 C2A H:HNI201 4.3 11.5 1.0 C3A H:HNI201 4.3 14.8 1.0 C2B H:HNI201 4.3 7.8 1.0 C3B H:HNI201 4.3 8.3 1.0 CG H:HIS92 4.4 10.8 1.0 CE1 H:HIS63 4.4 13.9 1.0 CD1 H:LEU96 5.0 13.4 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