Nickel 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:

Iron

(Fe)

4 atoms

The binding sites of Nickel 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 Nickel atom.
In total 4 binding sites of Nickel 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 Nickel binding site number: 1; 2; 3; 4;

Nickel 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 Nickel with other atoms in the Ni 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 A:Ni201 b:11.2 occ:1.00 NI A:HNI201 0.0 11.2 1.0 NC A:HNI201 2.0 11.5 1.0 NB A:HNI201 2.0 10.8 1.0 NA A:HNI201 2.0 11.5 1.0 ND A:HNI201 2.0 12.6 1.0 C4B A:HNI201 3.0 11.9 1.0 C1C A:HNI201 3.0 13.1 1.0 C4C A:HNI201 3.0 12.7 1.0 C1A A:HNI201 3.0 14.9 1.0 C1D A:HNI201 3.1 11.6 1.0 C4D A:HNI201 3.1 15.5 1.0 C4A A:HNI201 3.1 10.3 1.0 C1B A:HNI201 3.1 13.0 1.0 CHC A:HNI201 3.4 12.5 1.0 CHA A:HNI201 3.4 14.1 1.0 CHD A:HNI201 3.4 13.5 1.0 CE1 A:HIS87 3.4 16.4 1.0 CHB A:HNI201 3.4 12.9 1.0 NE2 A:HIS87 3.7 14.8 1.0 CE1 A:HIS58 3.7 19.1 1.0 NE2 A:HIS58 3.8 19.8 1.0 C2C A:HNI201 4.3 13.3 1.0 C3B A:HNI201 4.3 10.5 1.0 C3C A:HNI201 4.3 13.5 1.0 C2A A:HNI201 4.3 16.0 1.0 C2B A:HNI201 4.3 10.9 1.0 C2D A:HNI201 4.3 17.0 1.0 C3A A:HNI201 4.3 15.0 1.0 C3D A:HNI201 4.3 17.1 1.0 CD1 A:LEU91 4.4 15.5 1.0 CG2 A:VAL62 4.6 11.9 1.0 ND1 A:HIS87 4.7 14.3 1.0 CD2 A:HIS87 5.0 13.8 1.0

Nickel 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 Nickel with other atoms in the Ni 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 C:Ni201 b:8.2 occ:1.00 NI C:HNI201 0.0 8.2 1.0 NA C:HNI201 2.0 8.9 1.0 NC C:HNI201 2.0 9.5 1.0 ND C:HNI201 2.0 11.5 1.0 NB C:HNI201 2.0 10.6 1.0 C1A C:HNI201 3.0 11.9 1.0 C1C C:HNI201 3.0 10.7 1.0 C4B C:HNI201 3.0 9.8 1.0 C4A C:HNI201 3.0 10.2 1.0 C4D C:HNI201 3.0 9.3 1.0 C1B C:HNI201 3.1 8.7 1.0 C4C C:HNI201 3.1 7.3 1.0 C1D C:HNI201 3.1 9.9 1.0 CHA C:HNI201 3.4 9.4 1.0 CHC C:HNI201 3.4 11.3 1.0 CHB C:HNI201 3.4 9.4 1.0 CHD C:HNI201 3.4 8.7 1.0 C C:CMO202 3.5 34.7 1.0 CE1 C:HIS87 3.5 10.2 1.0 NE2 C:HIS87 3.7 12.2 1.0 O C:CMO202 3.7 44.8 1.0 NE2 C:HIS58 3.9 15.3 1.0 CE1 C:HIS58 4.0 14.8 1.0 C2A C:HNI201 4.2 13.5 1.0 C3A C:HNI201 4.2 13.8 1.0 C2C C:HNI201 4.3 10.1 1.0 C3B C:HNI201 4.3 10.0 1.0 C3C C:HNI201 4.3 9.9 1.0 C2B C:HNI201 4.3 9.1 1.0 C3D C:HNI201 4.3 10.1 1.0 C2D C:HNI201 4.3 11.9 1.0 CD1 C:LEU91 4.5 13.6 1.0 CG2 C:VAL62 4.6 10.9 1.0 ND1 C:HIS87 4.7 11.0 1.0 CD2 C:HIS87 5.0 13.2 1.0

Nickel 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 Nickel with other atoms in the Ni 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 E:Ni201 b:9.1 occ:1.00 NI E:HNI201 0.0 9.1 1.0 NC E:HNI201 2.0 8.0 1.0 NB E:HNI201 2.0 12.5 1.0 ND E:HNI201 2.0 11.6 1.0 NA E:HNI201 2.0 9.9 1.0 C4C E:HNI201 3.0 9.0 1.0 C1D E:HNI201 3.0 9.7 1.0 C4A E:HNI201 3.0 10.3 1.0 C1B E:HNI201 3.0 8.7 1.0 C1C E:HNI201 3.1 12.4 1.0 C4B E:HNI201 3.1 11.1 1.0 C1A E:HNI201 3.1 15.7 1.0 C4D E:HNI201 3.1 10.2 1.0 C E:CMO202 3.2 33.2 1.0 CHD E:HNI201 3.4 9.8 1.0 CHB E:HNI201 3.4 12.2 1.0 CHC E:HNI201 3.4 13.1 1.0 CHA E:HNI201 3.4 10.8 1.0 CE1 E:HIS87 3.5 11.5 1.0 NE2 E:HIS87 3.7 14.4 1.0 O E:CMO202 3.8 54.2 1.0 NE2 E:HIS58 3.9 17.3 1.0 CE1 E:HIS58 4.0 23.7 1.0 C3C E:HNI201 4.2 8.8 1.0 C2D E:HNI201 4.2 10.2 1.0 C3A E:HNI201 4.2 13.9 1.0 C2C E:HNI201 4.2 11.6 1.0 C2B E:HNI201 4.3 10.9 1.0 C3D E:HNI201 4.3 10.8 1.0 C2A E:HNI201 4.3 15.9 1.0 C3B E:HNI201 4.3 10.3 1.0 CD1 E:LEU91 4.4 14.6 1.0 CG2 E:VAL62 4.5 12.8 1.0 ND1 E:HIS87 4.7 12.2 1.0

Nickel 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 Nickel with other atoms in the Ni 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 G:Ni201 b:7.8 occ:1.00 NI G:HNI201 0.0 7.8 1.0 NC G:HNI201 2.0 6.8 1.0 NB G:HNI201 2.0 9.7 1.0 NA G:HNI201 2.0 8.0 1.0 ND G:HNI201 2.0 8.7 1.0 C1C G:HNI201 3.0 9.4 1.0 C4B G:HNI201 3.0 8.0 1.0 C4A G:HNI201 3.0 9.1 1.0 C1B G:HNI201 3.0 9.1 1.0 C1A G:HNI201 3.0 9.2 1.0 C4C G:HNI201 3.0 8.2 1.0 C4D G:HNI201 3.0 9.7 1.0 C1D G:HNI201 3.1 8.3 1.0 CHC G:HNI201 3.4 8.9 1.0 O G:CMO202 3.4 45.3 1.0 CHB G:HNI201 3.4 9.5 1.0 CHA G:HNI201 3.4 10.0 1.0 CHD G:HNI201 3.4 8.5 1.0 CE1 G:HIS87 3.5 12.1 1.0 C G:CMO202 3.5 33.6 1.0 NE2 G:HIS87 3.7 11.5 1.0 CE1 G:HIS58 3.7 13.3 1.0 NE2 G:HIS58 4.0 14.9 1.0 C2C G:HNI201 4.2 8.4 1.0 C3A G:HNI201 4.2 10.5 1.0 C3B G:HNI201 4.2 10.0 1.0 C2A G:HNI201 4.2 11.5 1.0 C3C G:HNI201 4.2 8.9 1.0 C2B G:HNI201 4.2 7.6 1.0 C3D G:HNI201 4.3 9.6 1.0 C2D G:HNI201 4.3 11.1 1.0 CD1 G:LEU91 4.5 12.3 1.0 CG2 G:VAL62 4.6 12.5 1.0 ND1 G:HIS87 4.7 12.4 1.0 ND1 G:HIS58 5.0 15.4 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