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

The structure of Closslinked Alpha(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6kah 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)	19.85 / 1.45
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.529, 94.032, 99.793, 90.00, 102.07, 90.00
R / Rfree (%)	17.3 / 19.6

The structure of Closslinked Alpha(Ni)-Beta(Fe-Co) 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark (pdb code 6kah). 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6kah:
Jump to Nickel binding site number: 1; 2; 3; 4;

Nickel binding site 1 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe-Co) 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni201 b:9.6 occ:1.00 NI A:HNI201 0.0 9.6 1.0 NC A:HNI201 2.0 10.1 1.0 NA A:HNI201 2.0 10.2 1.0 ND A:HNI201 2.0 10.8 1.0 NB A:HNI201 2.0 9.3 1.0 C4B A:HNI201 3.0 8.9 1.0 C1C A:HNI201 3.0 10.8 1.0 C4C A:HNI201 3.0 10.1 1.0 C1D A:HNI201 3.0 10.4 1.0 C4A A:HNI201 3.1 9.2 1.0 C1A A:HNI201 3.1 13.2 1.0 C4D A:HNI201 3.1 13.3 1.0 C1B A:HNI201 3.1 11.2 1.0 CHC A:HNI201 3.4 10.1 1.0 CHD A:HNI201 3.4 11.2 1.0 CHA A:HNI201 3.4 12.7 1.0 CHB A:HNI201 3.4 10.9 1.0 CE1 A:HIS87 3.4 13.9 1.0 NE2 A:HIS87 3.7 12.3 1.0 CE1 A:HIS58 3.7 21.0 1.0 NE2 A:HIS58 3.8 19.1 1.0 C2C A:HNI201 4.3 10.9 1.0 C3C A:HNI201 4.3 11.3 1.0 C3A A:HNI201 4.3 12.9 1.0 C3B A:HNI201 4.3 9.2 1.0 C2A A:HNI201 4.3 12.9 1.0 C2D A:HNI201 4.3 15.2 1.0 C2B A:HNI201 4.3 10.3 1.0 C3D A:HNI201 4.3 14.9 1.0 CD1 A:LEU91 4.4 15.0 1.0 CG2 A:VAL62 4.5 9.6 1.0 ND1 A:HIS87 4.7 13.4 1.0 ND1 A:HIS58 5.0 18.1 1.0 CD2 A:HIS87 5.0 13.2 1.0

Nickel binding site 2 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe-Co) 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ C:Ni201 b:7.2 occ:1.00 NI C:HNI201 0.0 7.2 1.0 NC C:HNI201 2.0 8.0 1.0 NA C:HNI201 2.0 7.3 1.0 NB C:HNI201 2.0 9.2 1.0 ND C:HNI201 2.0 9.6 1.0 C1A C:HNI201 3.0 10.8 1.0 C1C C:HNI201 3.0 9.3 1.0 C4B C:HNI201 3.0 8.4 1.0 C4A C:HNI201 3.0 9.4 1.0 C1B C:HNI201 3.0 7.6 1.0 C4C C:HNI201 3.0 7.6 1.0 C1D C:HNI201 3.0 9.1 1.0 C4D C:HNI201 3.0 7.8 1.0 CHA C:HNI201 3.4 8.9 1.0 CHC C:HNI201 3.4 9.7 1.0 CHD C:HNI201 3.4 7.6 1.0 CHB C:HNI201 3.4 8.1 1.0 CE1 C:HIS87 3.4 10.8 1.0 NE2 C:HIS87 3.7 10.9 1.0 NE2 C:HIS58 3.8 15.3 1.0 CE1 C:HIS58 4.0 18.4 1.0 C2A C:HNI201 4.2 12.8 1.0 C3A C:HNI201 4.3 12.1 1.0 C2C C:HNI201 4.3 9.6 1.0 C3C C:HNI201 4.3 9.3 1.0 C2B C:HNI201 4.3 7.3 1.0 C3B C:HNI201 4.3 8.4 1.0 C2D C:HNI201 4.3 9.3 1.0 C3D C:HNI201 4.3 9.2 1.0 CG2 C:VAL62 4.5 8.8 1.0 CD1 C:LEU91 4.5 11.0 1.0 ND1 C:HIS87 4.7 10.6 1.0 CD2 C:HIS87 5.0 10.7 1.0

Nickel binding site 3 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe-Co) 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ E:Ni201 b:7.9 occ:1.00 NI E:HNI201 0.0 7.9 1.0 NA E:HNI201 2.0 9.4 1.0 ND E:HNI201 2.0 9.3 1.0 NC E:HNI201 2.0 6.9 1.0 NB E:HNI201 2.0 10.8 1.0 C1D E:HNI201 3.0 8.0 1.0 C4A E:HNI201 3.0 8.3 1.0 C4C E:HNI201 3.0 8.8 1.0 C1B E:HNI201 3.0 8.5 1.0 C1A E:HNI201 3.0 12.4 1.0 C1C E:HNI201 3.1 9.2 1.0 C4D E:HNI201 3.1 10.1 1.0 C4B E:HNI201 3.1 10.6 1.0 CHD E:HNI201 3.4 9.0 1.0 CHB E:HNI201 3.4 10.9 1.0 CHC E:HNI201 3.4 10.7 1.0 CHA E:HNI201 3.4 10.0 1.0 CE1 E:HIS87 3.5 9.5 1.0 NE2 E:HIS87 3.7 11.6 1.0 NE2 E:HIS58 3.8 18.5 1.0 CE1 E:HIS58 4.1 22.4 1.0 C2D E:HNI201 4.2 9.4 1.0 C3A E:HNI201 4.2 10.8 1.0 C2A E:HNI201 4.3 14.1 1.0 C3C E:HNI201 4.3 8.1 1.0 C2C E:HNI201 4.3 9.8 1.0 C3D E:HNI201 4.3 9.3 1.0 C2B E:HNI201 4.3 8.3 1.0 C3B E:HNI201 4.3 9.6 1.0 CD1 E:LEU91 4.4 14.2 1.0 CG2 E:VAL62 4.4 10.2 1.0 ND1 E:HIS87 4.7 11.4 1.0

Nickel binding site 4 out of 4 in the Closslinked Alpha(Ni)-Beta(Fe-Co) 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(Ni)-Beta(Fe-Co) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark within 5.0Å range: probe atom residue distance (Å) B Occ G:Ni201 b:7.0 occ:1.00 NI G:HNI201 0.0 7.0 1.0 NC G:HNI201 2.0 6.2 1.0 NB G:HNI201 2.0 8.4 1.0 ND G:HNI201 2.0 8.2 1.0 NA G:HNI201 2.0 8.0 1.0 C4C G:HNI201 3.0 7.0 1.0 C1C G:HNI201 3.0 7.1 1.0 C4B G:HNI201 3.0 7.4 1.0 C1D G:HNI201 3.0 8.6 1.0 C1B G:HNI201 3.0 7.8 1.0 C4A G:HNI201 3.0 8.3 1.0 C1A G:HNI201 3.0 8.7 1.0 C4D G:HNI201 3.1 9.8 1.0 CHC G:HNI201 3.4 8.4 1.0 CHD G:HNI201 3.4 7.8 1.0 CHB G:HNI201 3.4 8.6 1.0 CHA G:HNI201 3.4 9.0 1.0 CE1 G:HIS87 3.5 10.8 1.0 CE1 G:HIS58 3.6 11.9 1.0 NE2 G:HIS87 3.7 10.2 1.0 NE2 G:HIS58 3.9 11.9 1.0 C2C G:HNI201 4.2 7.1 1.0 C3C G:HNI201 4.2 8.1 1.0 C3B G:HNI201 4.3 9.5 1.0 C2B G:HNI201 4.3 7.6 1.0 C2A G:HNI201 4.3 10.2 1.0 C3A G:HNI201 4.3 9.7 1.0 C2D G:HNI201 4.3 9.3 1.0 C3D G:HNI201 4.3 9.3 1.0 CD1 G:LEU91 4.5 11.5 1.0 CG2 G:VAL62 4.5 9.8 1.0 ND1 G:HIS87 4.7 10.7 1.0 ND1 G:HIS58 4.9 14.2 1.0 CD2 G:HIS87 5.0 9.6 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