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

The structure of Closslinked Alpha(Ni)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6lcw 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)	19.81 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.771, 94.419, 100.430, 90.00, 102.06, 90.00
R / Rfree (%)	19.6 / 21.8

The binding sites of Nickel atom in the Closslinked Alpha(Ni)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark (pdb code 6lcw). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 8 binding sites of Nickel where determined in the Closslinked Alpha(Ni)-Beta(Ni) Human Hemoglobin A in the T Quaternary Structure at 95 K: Dark, PDB code: 6lcw:
Jump to Nickel binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Nickel binding site 1 out of 8 in the Closslinked Alpha(Ni)-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(Ni)-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 A:Ni201 b:9.1 occ:1.00 NI A:HNI201 0.0 9.1 1.0 NC A:HNI201 2.0 9.2 1.0 ND A:HNI201 2.0 12.0 1.0 NA A:HNI201 2.0 10.6 1.0 NB A:HNI201 2.0 8.2 1.0 C4C A:HNI201 3.0 9.5 1.0 C1D A:HNI201 3.0 10.6 1.0 C1C A:HNI201 3.0 10.3 1.0 C4B A:HNI201 3.1 7.8 1.0 C1A A:HNI201 3.1 12.4 1.0 C4A A:HNI201 3.1 11.4 1.0 C4D A:HNI201 3.1 13.0 1.0 C1B A:HNI201 3.1 9.7 1.0 CHD A:HNI201 3.4 9.6 1.0 CHC A:HNI201 3.4 10.3 1.0 CE1 A:HIS87 3.4 12.9 1.0 CHA A:HNI201 3.4 12.0 1.0 CHB A:HNI201 3.5 12.4 1.0 CE1 A:HIS58 3.6 22.8 1.0 NE2 A:HIS87 3.6 12.3 1.0 NE2 A:HIS58 3.9 17.0 1.0 C3C A:HNI201 4.2 11.0 1.0 C2C A:HNI201 4.3 9.1 1.0 C2D A:HNI201 4.3 12.3 1.0 C2A A:HNI201 4.3 12.6 1.0 C3D A:HNI201 4.3 12.2 1.0 C3A A:HNI201 4.3 12.2 1.0 C3B A:HNI201 4.3 10.7 1.0 C2B A:HNI201 4.3 8.2 1.0 CG2 A:VAL62 4.5 12.7 1.0 CD1 A:LEU91 4.5 15.1 1.0 ND1 A:HIS87 4.6 13.0 1.0 ND1 A:HIS58 4.8 35.0 1.0 CD2 A:HIS87 5.0 12.0 1.0

Nickel binding site 2 out of 8 in the Closslinked Alpha(Ni)-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(Ni)-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:6.5 occ:1.00 NI B:HNI201 0.0 6.5 1.0 NB B:HNI201 2.0 8.0 1.0 NC B:HNI201 2.0 5.9 1.0 ND B:HNI201 2.1 9.3 1.0 NA B:HNI201 2.1 6.6 1.0 NE2 B:HIS92 2.2 6.0 1.0 C4B B:HNI201 3.1 6.1 1.0 C1C B:HNI201 3.1 5.4 1.0 C4C B:HNI201 3.1 5.8 1.0 C1B B:HNI201 3.1 7.8 1.0 C1A B:HNI201 3.1 7.3 1.0 C4D B:HNI201 3.1 7.1 1.0 C1D B:HNI201 3.1 7.6 1.0 C4A B:HNI201 3.1 6.7 1.0 CE1 B:HIS92 3.1 7.8 1.0 CD2 B:HIS92 3.2 6.2 1.0 CHD B:HNI201 3.4 7.3 1.0 CHC B:HNI201 3.4 6.5 1.0 CHA B:HNI201 3.4 7.8 1.0 CHB B:HNI201 3.5 8.3 1.0 CG2 B:VAL67 4.0 9.6 1.0 NE2 B:HIS63 4.1 18.8 1.0 ND1 B:HIS92 4.2 6.9 1.0 C3B B:HNI201 4.3 8.4 1.0 C2B B:HNI201 4.3 6.9 1.0 C2C B:HNI201 4.3 6.2 1.0 C3C B:HNI201 4.3 7.0 1.0 C3D B:HNI201 4.3 7.4 1.0 C2D B:HNI201 4.3 7.1 1.0 C2A B:HNI201 4.3 8.9 1.0 C3A B:HNI201 4.3 7.7 1.0 CG B:HIS92 4.3 6.9 1.0 CE1 B:HIS63 4.8 7.8 1.0 CD1 B:LEU96 4.9 8.7 1.0

Nickel binding site 3 out of 8 in the Closslinked Alpha(Ni)-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(Ni)-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 C:Ni201 b:7.2 occ:1.00 NI C:HNI201 0.0 7.2 1.0 NC C:HNI201 2.0 6.2 1.0 NA C:HNI201 2.0 8.0 1.0 ND C:HNI201 2.0 9.6 1.0 NB C:HNI201 2.0 11.7 1.0 C1C C:HNI201 3.0 7.1 1.0 C4C C:HNI201 3.0 6.8 1.0 C4B C:HNI201 3.0 8.4 1.0 C1A C:HNI201 3.0 8.2 1.0 C4A C:HNI201 3.0 10.9 1.0 C4D C:HNI201 3.0 9.2 1.0 C1D C:HNI201 3.0 7.6 1.0 C1B C:HNI201 3.1 9.1 1.0 CHC C:HNI201 3.4 11.4 1.0 CE1 C:HIS87 3.4 10.5 1.0 CHD C:HNI201 3.4 7.5 1.0 CHA C:HNI201 3.4 9.7 1.0 CHB C:HNI201 3.4 8.6 1.0 NE2 C:HIS87 3.6 11.6 1.0 NE2 C:HIS58 3.8 23.3 1.0 CE1 C:HIS58 4.1 18.9 1.0 C2C C:HNI201 4.2 7.0 1.0 C3C C:HNI201 4.2 7.3 1.0 C3A C:HNI201 4.2 9.6 1.0 C2A C:HNI201 4.3 11.5 1.0 C3B C:HNI201 4.3 10.9 1.0 C2D C:HNI201 4.3 8.1 1.0 C3D C:HNI201 4.3 11.7 1.0 C2B C:HNI201 4.3 8.4 1.0 CG2 C:VAL62 4.5 12.3 1.0 CD1 C:LEU91 4.5 13.1 1.0 ND1 C:HIS87 4.6 11.5 1.0 CD2 C:HIS87 5.0 8.6 1.0

Nickel binding site 4 out of 8 in the Closslinked Alpha(Ni)-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(Ni)-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:Ni502 b:73.9 occ:1.00 NI D:HNI502 0.0 73.9 1.0 ND D:HNI502 2.0 11.2 1.0 NB D:HNI502 2.1 9.3 1.0 NC D:HNI502 2.1 12.8 1.0 NA D:HNI502 2.1 12.6 1.0 NE2 D:HIS92 2.5 9.8 1.0 C1D D:HNI502 3.0 17.0 1.0 C4C D:HNI502 3.1 16.1 1.0 C4A D:HNI502 3.1 20.4 1.0 C4D D:HNI502 3.1 20.4 1.0 C1C D:HNI502 3.1 13.3 1.0 C1B D:HNI502 3.1 14.3 1.0 C4B D:HNI502 3.1 13.8 1.0 C1A D:HNI502 3.1 13.5 1.0 CE1 D:HIS92 3.4 14.7 1.0 CHD D:HNI502 3.4 16.5 1.0 CHB D:HNI502 3.4 14.0 1.0 CHC D:HNI502 3.4 10.4 1.0 CHA D:HNI502 3.5 12.3 1.0 CD2 D:HIS92 3.6 9.8 1.0 CG2 D:VAL67 3.6 15.1 1.0 NE2 D:HIS63 3.9 25.3 1.0 C2D D:HNI502 4.3 20.5 1.0 C3C D:HNI502 4.3 18.2 1.0 C2C D:HNI502 4.3 18.1 1.0 C3D D:HNI502 4.3 16.3 1.0 C3A D:HNI502 4.3 18.9 1.0 C2A D:HNI502 4.3 15.3 1.0 C2B D:HNI502 4.3 15.8 1.0 C3B D:HNI502 4.3 16.1 1.0 CE1 D:HIS63 4.3 22.4 1.0 ND1 D:HIS92 4.6 13.4 1.0 CG D:HIS92 4.7 12.1 1.0 CB D:VAL67 4.9 13.5 1.0 CG1 D:VAL67 5.0 21.2 1.0

Nickel binding site 5 out of 8 in the Closslinked Alpha(Ni)-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 5 of Closslinked Alpha(Ni)-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 E:Ni201 b:8.1 occ:1.00 NI E:HNI201 0.0 8.1 1.0 ND E:HNI201 2.0 10.7 1.0 NB E:HNI201 2.0 12.7 1.0 NC E:HNI201 2.0 7.0 1.0 NA E:HNI201 2.0 7.5 1.0 C4A E:HNI201 3.0 8.3 1.0 C1B E:HNI201 3.0 8.6 1.0 C1D E:HNI201 3.0 7.7 1.0 C4C E:HNI201 3.0 7.1 1.0 C4D E:HNI201 3.1 9.7 1.0 C4B E:HNI201 3.1 8.5 1.0 C1C E:HNI201 3.1 8.3 1.0 C1A E:HNI201 3.1 11.7 1.0 CHB E:HNI201 3.4 11.4 1.0 CHD E:HNI201 3.4 9.7 1.0 CHA E:HNI201 3.4 9.9 1.0 CHC E:HNI201 3.5 8.7 1.0 CE1 E:HIS87 3.5 9.9 1.0 NE2 E:HIS87 3.7 11.1 1.0 NE2 E:HIS58 3.8 21.7 1.0 CE1 E:HIS58 4.0 21.7 1.0 C2D E:HNI201 4.2 10.8 1.0 C3A E:HNI201 4.2 13.0 1.0 C2B E:HNI201 4.2 9.3 1.0 C3D E:HNI201 4.3 10.3 1.0 C3C E:HNI201 4.3 8.4 1.0 C3B E:HNI201 4.3 10.5 1.0 C2A E:HNI201 4.3 13.6 1.0 C2C E:HNI201 4.3 8.5 1.0 CD1 E:LEU91 4.4 12.6 1.0 CG2 E:VAL62 4.5 19.9 1.0 ND1 E:HIS87 4.7 9.6 1.0

Nickel binding site 6 out of 8 in the Closslinked Alpha(Ni)-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 6 of Closslinked Alpha(Ni)-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:6.8 occ:1.00 NI F:HNI201 0.0 6.8 1.0 NC F:HNI201 2.0 7.2 1.0 ND F:HNI201 2.0 9.3 1.0 NA F:HNI201 2.1 7.8 1.0 NB F:HNI201 2.1 6.7 1.0 NE2 F:HIS92 2.2 6.0 1.0 C4C F:HNI201 3.1 6.4 1.0 C1D F:HNI201 3.1 6.9 1.0 C1C F:HNI201 3.1 6.1 1.0 C4B F:HNI201 3.1 6.8 1.0 C4D F:HNI201 3.1 7.1 1.0 C4A F:HNI201 3.1 6.8 1.0 C1A F:HNI201 3.1 9.4 1.0 C1B F:HNI201 3.1 7.0 1.0 CE1 F:HIS92 3.1 9.6 1.0 CD2 F:HIS92 3.2 6.1 1.0 CHD F:HNI201 3.4 7.8 1.0 CHC F:HNI201 3.4 7.7 1.0 CHB F:HNI201 3.5 7.4 1.0 CHA F:HNI201 3.5 8.7 1.0 CG2 F:VAL67 4.0 10.0 1.0 NE2 F:HIS63 4.2 15.6 1.0 ND1 F:HIS92 4.2 6.8 1.0 C2D F:HNI201 4.3 10.2 1.0 C2C F:HNI201 4.3 6.2 1.0 C3C F:HNI201 4.3 7.3 1.0 C3D F:HNI201 4.3 10.1 1.0 C3A F:HNI201 4.3 10.4 1.0 C2A F:HNI201 4.3 9.0 1.0 C3B F:HNI201 4.3 7.8 1.0 C2B F:HNI201 4.3 7.1 1.0 CG F:HIS92 4.3 6.4 1.0 CE1 F:HIS63 4.7 10.6 1.0 CD1 F:LEU96 4.9 8.5 1.0

Nickel binding site 7 out of 8 in the Closslinked Alpha(Ni)-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 7 of Closslinked Alpha(Ni)-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 G:Ni201 b:6.9 occ:1.00 NI G:HNI201 0.0 6.9 1.0 NB G:HNI201 2.0 7.8 1.0 NC G:HNI201 2.0 6.3 1.0 NA G:HNI201 2.0 7.9 1.0 ND G:HNI201 2.0 8.2 1.0 C4B G:HNI201 3.0 6.8 1.0 C1C G:HNI201 3.0 7.0 1.0 C4A G:HNI201 3.0 8.3 1.0 C1B G:HNI201 3.0 10.2 1.0 C4D G:HNI201 3.0 10.2 1.0 C1A G:HNI201 3.1 10.1 1.0 C1D G:HNI201 3.1 8.0 1.0 C4C G:HNI201 3.1 6.6 1.0 CHC G:HNI201 3.4 8.5 1.0 CHA G:HNI201 3.4 9.5 1.0 CHB G:HNI201 3.4 8.8 1.0 CE1 G:HIS87 3.4 9.9 1.0 CHD G:HNI201 3.4 9.4 1.0 NE2 G:HIS87 3.7 10.4 1.0 CE1 G:HIS58 3.7 15.7 1.0 NE2 G:HIS58 4.0 12.7 1.0 C3B G:HNI201 4.2 8.1 1.0 C3A G:HNI201 4.3 10.7 1.0 C2B G:HNI201 4.3 9.0 1.0 C2C G:HNI201 4.3 6.5 1.0 C2A G:HNI201 4.3 11.2 1.0 C3D G:HNI201 4.3 8.3 1.0 C2D G:HNI201 4.3 7.7 1.0 C3C G:HNI201 4.3 6.5 1.0 CG2 G:VAL62 4.5 10.1 1.0 CD1 G:LEU91 4.5 12.0 1.0 ND1 G:HIS87 4.7 10.2 1.0 CD2 G:HIS87 5.0 9.2 1.0 ND1 G:HIS58 5.0 12.0 1.0

Nickel binding site 8 out of 8 in the Closslinked Alpha(Ni)-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 8 of Closslinked Alpha(Ni)-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:9.7 occ:1.00 NI H:HNI201 0.0 9.7 1.0 NC H:HNI201 2.0 8.4 1.0 ND H:HNI201 2.1 12.1 1.0 NA H:HNI201 2.1 13.2 1.0 NB H:HNI201 2.1 12.0 1.0 NE2 H:HIS92 2.2 10.1 1.0 C4C H:HNI201 3.1 8.3 1.0 C1C H:HNI201 3.1 9.4 1.0 C1D H:HNI201 3.1 10.3 1.0 C4A H:HNI201 3.1 10.9 1.0 C1B H:HNI201 3.1 12.1 1.0 C4D H:HNI201 3.1 12.1 1.0 C1A H:HNI201 3.1 11.0 1.0 C4B H:HNI201 3.1 11.8 1.0 CE1 H:HIS92 3.2 14.9 1.0 CD2 H:HIS92 3.2 10.5 1.0 CHD H:HNI201 3.4 9.7 1.0 CHB H:HNI201 3.4 12.0 1.0 CHC H:HNI201 3.4 8.8 1.0 CHA H:HNI201 3.4 12.0 1.0 CG2 H:VAL67 4.1 11.0 1.0 NE2 H:HIS63 4.1 21.6 1.0 C2C H:HNI201 4.3 10.9 1.0 C2D H:HNI201 4.3 13.8 1.0 C3D H:HNI201 4.3 12.5 1.0 C3C H:HNI201 4.3 8.8 1.0 C3A H:HNI201 4.3 13.3 1.0 C2A H:HNI201 4.3 13.3 1.0 C2B H:HNI201 4.3 10.3 1.0 C3B H:HNI201 4.3 12.1 1.0 ND1 H:HIS92 4.3 13.2 1.0 CG H:HIS92 4.4 11.0 1.0 CE1 H:HIS63 4.6 11.0 1.0 CD1 H:LEU96 4.9 13.5 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