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

Protein crystallography data

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

Other elements in 6ka9:

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:

Nickel (Ni) 4 atoms

Iron Binding Sites:

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

Iron binding site 1 out of 4 in 6ka9

Go back to Iron Binding Sites List in 6ka9
Iron 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 Iron with other atoms in the Fe 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
A:Fe201

b:8.8
occ:1.00
FE A:HEM201 0.0 8.8 1.0
C A:CMO202 1.8 8.8 1.0
NC A:HEM201 2.0 9.6 1.0
ND A:HEM201 2.0 8.6 1.0
NA A:HEM201 2.0 8.4 1.0
NB A:HEM201 2.0 7.1 1.0
NE2 A:HIS87 2.3 9.2 1.0
C4C A:HEM201 3.0 8.8 1.0
C1C A:HEM201 3.0 9.4 1.0
O A:CMO202 3.0 12.7 1.0
C1D A:HEM201 3.0 8.8 1.0
C1A A:HEM201 3.1 10.8 1.0
C4B A:HEM201 3.1 7.2 1.0
C4A A:HEM201 3.1 8.4 1.0
C4D A:HEM201 3.1 9.9 1.0
C1B A:HEM201 3.1 8.4 1.0
CE1 A:HIS87 3.2 11.0 1.0
CD2 A:HIS87 3.3 8.7 1.0
CHC A:HEM201 3.4 9.2 1.0
CHD A:HEM201 3.4 9.3 1.0
CHA A:HEM201 3.4 11.5 1.0
CHB A:HEM201 3.4 8.5 1.0
C2C A:HEM201 4.2 9.9 1.0
C3C A:HEM201 4.2 9.0 1.0
C2D A:HEM201 4.3 10.5 1.0
C3D A:HEM201 4.3 10.0 1.0
C2A A:HEM201 4.3 11.7 1.0
C3A A:HEM201 4.3 10.0 1.0
C3B A:HEM201 4.3 8.4 1.0
C2B A:HEM201 4.3 9.3 1.0
ND1 A:HIS87 4.3 10.6 1.0
NE2 A:HIS58 4.4 12.1 1.0
CG A:HIS87 4.4 11.0 1.0
CD1 A:LEU91 5.0 10.9 1.0

Iron binding site 2 out of 4 in 6ka9

Go back to Iron Binding Sites List in 6ka9
Iron 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 Iron with other atoms in the Fe 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
C:Fe201

b:7.7
occ:1.00
FE C:HEM201 0.0 7.7 1.0
C C:CMO202 1.8 8.5 1.0
NC C:HEM201 2.0 5.5 1.0
NA C:HEM201 2.0 7.8 1.0
ND C:HEM201 2.0 8.8 1.0
NB C:HEM201 2.0 8.5 1.0
NE2 C:HIS87 2.3 10.1 1.0
C4C C:HEM201 3.0 6.2 1.0
C1C C:HEM201 3.0 6.8 1.0
O C:CMO202 3.0 11.9 1.0
C1A C:HEM201 3.0 7.7 1.0
C4B C:HEM201 3.0 6.4 1.0
C1D C:HEM201 3.0 8.3 1.0
C4A C:HEM201 3.0 9.6 1.0
C4D C:HEM201 3.1 7.2 1.0
C1B C:HEM201 3.1 7.5 1.0
CE1 C:HIS87 3.2 10.5 1.0
CD2 C:HIS87 3.3 8.6 1.0
CHC C:HEM201 3.4 7.8 1.0
CHA C:HEM201 3.4 7.3 1.0
CHD C:HEM201 3.4 7.2 1.0
CHB C:HEM201 3.4 10.2 1.0
C2C C:HEM201 4.2 8.7 1.0
C3C C:HEM201 4.2 6.7 1.0
C2A C:HEM201 4.3 9.5 1.0
C3A C:HEM201 4.3 7.9 1.0
C2D C:HEM201 4.3 7.5 1.0
C3D C:HEM201 4.3 7.7 1.0
C3B C:HEM201 4.3 8.6 1.0
C2B C:HEM201 4.3 6.8 1.0
NE2 C:HIS58 4.3 11.3 1.0
ND1 C:HIS87 4.4 9.7 1.0
CG C:HIS87 4.5 8.6 1.0
CD1 C:LEU91 4.8 10.6 1.0
CG2 C:VAL62 5.0 10.4 1.0

Iron binding site 3 out of 4 in 6ka9

Go back to Iron Binding Sites List in 6ka9
Iron 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 Iron with other atoms in the Fe 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
E:Fe201

b:7.8
occ:1.00
FE E:HEM201 0.0 7.8 1.0
C E:CMO202 1.8 9.5 1.0
NC E:HEM201 2.0 6.2 1.0
ND E:HEM201 2.0 8.0 1.0
NA E:HEM201 2.0 7.1 1.0
NB E:HEM201 2.0 8.1 1.0
NE2 E:HIS87 2.3 9.1 1.0
C4C E:HEM201 3.0 5.4 1.0
O E:CMO202 3.0 11.8 1.0
C1D E:HEM201 3.0 6.6 1.0
C1C E:HEM201 3.0 6.5 1.0
C1A E:HEM201 3.0 8.0 1.0
C4A E:HEM201 3.1 7.3 1.0
C4B E:HEM201 3.1 7.2 1.0
C4D E:HEM201 3.1 6.5 1.0
C1B E:HEM201 3.1 7.3 1.0
CE1 E:HIS87 3.2 7.8 1.0
CD2 E:HIS87 3.3 8.9 1.0
CHD E:HEM201 3.4 8.3 1.0
CHC E:HEM201 3.4 7.9 1.0
CHA E:HEM201 3.4 7.0 1.0
CHB E:HEM201 3.4 7.4 1.0
C3C E:HEM201 4.2 7.7 1.0
C2C E:HEM201 4.2 7.5 1.0
C2A E:HEM201 4.3 8.8 1.0
C2D E:HEM201 4.3 7.5 1.0
C3D E:HEM201 4.3 8.5 1.0
C3A E:HEM201 4.3 9.8 1.0
C3B E:HEM201 4.3 8.1 1.0
C2B E:HEM201 4.3 8.1 1.0
ND1 E:HIS87 4.4 7.3 1.0
NE2 E:HIS58 4.4 21.3 1.0
CG E:HIS87 4.4 8.7 1.0
CD1 E:LEU91 4.9 9.2 1.0
CG2 E:VAL62 5.0 10.3 1.0

Iron binding site 4 out of 4 in 6ka9

Go back to Iron Binding Sites List in 6ka9
Iron 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 Iron with other atoms in the Fe 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
G:Fe201

b:6.8
occ:1.00
FE G:HEM201 0.0 6.8 1.0
C G:CMO202 1.8 7.6 1.0
NC G:HEM201 2.0 5.7 1.0
ND G:HEM201 2.0 6.1 1.0
NB G:HEM201 2.0 6.8 1.0
NA G:HEM201 2.0 5.2 1.0
NE2 G:HIS87 2.3 6.8 1.0
O G:CMO202 3.0 11.2 1.0
C1C G:HEM201 3.0 5.9 1.0
C4C G:HEM201 3.0 5.9 1.0
C4B G:HEM201 3.0 6.1 1.0
C1D G:HEM201 3.0 6.5 1.0
C4A G:HEM201 3.1 7.0 1.0
C1A G:HEM201 3.1 5.7 1.0
C4D G:HEM201 3.1 7.7 1.0
C1B G:HEM201 3.1 6.1 1.0
CE1 G:HIS87 3.2 8.7 1.0
CD2 G:HIS87 3.3 6.4 1.0
CHC G:HEM201 3.4 6.6 1.0
CHD G:HEM201 3.4 6.9 1.0
CHA G:HEM201 3.4 6.7 1.0
CHB G:HEM201 3.4 8.2 1.0
C2C G:HEM201 4.2 7.0 1.0
C3C G:HEM201 4.3 7.1 1.0
C2D G:HEM201 4.3 6.8 1.0
C3A G:HEM201 4.3 8.0 1.0
C2A G:HEM201 4.3 7.2 1.0
C3B G:HEM201 4.3 7.5 1.0
C3D G:HEM201 4.3 8.0 1.0
C2B G:HEM201 4.3 6.1 1.0
ND1 G:HIS87 4.3 8.1 1.0
NE2 G:HIS58 4.4 26.4 1.0
CG G:HIS87 4.4 6.6 1.0
CD1 G:LEU91 4.8 10.0 1.0
CG2 G:VAL62 5.0 8.4 1.0

Reference:

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
Page generated: Sun Dec 13 16:36:26 2020

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