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Iron in PDB 5x2s: Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.

Protein crystallography data

The structure of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5., PDB code: 5x2s was solved by M.Ohki, S.-Y.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.99 / 2.39
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.603, 54.598, 138.444, 90.00, 103.18, 90.00
R / Rfree (%) 24.5 / 28.8

Other elements in 5x2s:

The structure of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. also contains other interesting chemical elements:

Nickel (Ni) 6 atoms
Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. (pdb code 5x2s). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5., PDB code: 5x2s:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 1 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:66.9
occ:1.00
FE B:HEM201 0.0 66.9 1.0
NA B:HEM201 1.9 67.4 1.0
NB B:HEM201 1.9 65.2 1.0
ND B:HEM201 2.0 68.8 1.0
NC B:HEM201 2.0 66.7 1.0
NE2 B:HIS92 2.1 59.8 1.0
CE1 B:HIS92 2.9 59.5 1.0
C4B B:HEM201 2.9 64.8 1.0
C4D B:HEM201 3.0 70.0 1.0
C1A B:HEM201 3.0 68.7 1.0
C1B B:HEM201 3.0 65.3 1.0
C1D B:HEM201 3.0 70.0 1.0
C1C B:HEM201 3.0 65.8 1.0
C4A B:HEM201 3.0 66.9 1.0
C4C B:HEM201 3.0 68.1 1.0
CD2 B:HIS92 3.3 60.9 1.0
CHA B:HEM201 3.3 70.2 1.0
CHC B:HEM201 3.4 65.6 1.0
CHB B:HEM201 3.4 66.3 1.0
CHD B:HEM201 3.4 70.1 1.0
ND1 B:HIS92 4.1 60.9 1.0
C2A B:HEM201 4.2 69.3 1.0
C2B B:HEM201 4.2 64.6 1.0
C3A B:HEM201 4.2 68.3 1.0
C2C B:HEM201 4.2 67.0 1.0
C3B B:HEM201 4.2 64.6 1.0
C3D B:HEM201 4.3 72.1 1.0
C3C B:HEM201 4.3 68.3 1.0
CG B:HIS92 4.3 60.3 1.0
C2D B:HEM201 4.3 72.0 1.0
CG2 B:VAL67 4.6 63.5 1.0
CE1 B:HIS63 4.7 80.2 1.0

Iron binding site 2 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 2 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:78.3
occ:1.00
FE C:HEM201 0.0 78.3 1.0
NB C:HEM201 1.9 77.4 1.0
NA C:HEM201 1.9 78.8 1.0
NC C:HEM201 2.0 78.0 1.0
ND C:HEM201 2.0 79.2 1.0
NE2 C:HIS87 2.3 0.1 1.0
C1B C:HEM201 2.9 77.8 1.0
C4B C:HEM201 2.9 77.3 1.0
C1D C:HEM201 3.0 79.9 1.0
CE1 C:HIS87 3.0 0.2 1.0
C4D C:HEM201 3.0 80.1 1.0
C1C C:HEM201 3.0 77.4 1.0
C4A C:HEM201 3.0 78.6 1.0
C4C C:HEM201 3.0 78.7 1.0
C1A C:HEM201 3.0 79.5 1.0
CHC C:HEM201 3.3 77.8 1.0
CHB C:HEM201 3.4 78.5 1.0
CHD C:HEM201 3.4 80.0 1.0
CHA C:HEM201 3.4 80.5 1.0
CD2 C:HIS87 3.6 0.9 1.0
C2B C:HEM201 4.1 77.6 1.0
C3B C:HEM201 4.2 77.5 1.0
C2C C:HEM201 4.2 78.1 1.0
C3A C:HEM201 4.2 79.5 1.0
C2A C:HEM201 4.2 80.0 1.0
C3C C:HEM201 4.2 78.7 1.0
ND1 C:HIS87 4.3 0.8 1.0
C2D C:HEM201 4.3 81.2 1.0
C3D C:HEM201 4.3 81.5 1.0
CG C:HIS87 4.5 0.2 1.0
CG2 C:VAL62 4.7 92.1 1.0
CD2 C:LEU136 4.9 73.8 1.0

Iron binding site 3 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 3 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:56.5
occ:1.00
FE F:HEM201 0.0 56.5 1.0
ND F:HEM201 1.9 57.4 1.0
NC F:HEM201 1.9 56.1 1.0
NB F:HEM201 1.9 55.6 1.0
NA F:HEM201 2.0 57.2 1.0
NE2 F:HIS92 2.2 73.1 1.0
C1D F:HEM201 2.9 58.1 1.0
C4D F:HEM201 2.9 58.4 1.0
C1C F:HEM201 2.9 55.6 1.0
C4B F:HEM201 2.9 55.4 1.0
C1B F:HEM201 3.0 56.0 1.0
C4C F:HEM201 3.0 56.9 1.0
C1A F:HEM201 3.1 58.1 1.0
C4A F:HEM201 3.1 57.1 1.0
CD2 F:HIS92 3.2 73.9 1.0
CE1 F:HIS92 3.2 73.5 1.0
CHC F:HEM201 3.3 55.9 1.0
CHD F:HEM201 3.4 58.3 1.0
CHA F:HEM201 3.4 59.0 1.0
CHB F:HEM201 3.4 57.0 1.0
C2C F:HEM201 4.1 56.4 1.0
C2B F:HEM201 4.2 55.9 1.0
C3D F:HEM201 4.2 59.7 1.0
C2D F:HEM201 4.2 59.4 1.0
C3C F:HEM201 4.2 57.1 1.0
C3B F:HEM201 4.2 55.7 1.0
C3A F:HEM201 4.3 58.4 1.0
C2A F:HEM201 4.3 58.9 1.0
CG F:HIS92 4.3 73.3 1.0
CG2 F:VAL67 4.3 62.5 1.0
ND1 F:HIS92 4.4 75.0 1.0
NE2 F:HIS63 4.5 69.5 1.0

Iron binding site 4 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 4 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:68.6
occ:1.00
FE G:HEM201 0.0 68.6 1.0
ND G:HEM201 1.9 70.2 1.0
NB G:HEM201 1.9 67.3 1.0
NA G:HEM201 1.9 69.4 1.0
NC G:HEM201 2.0 68.3 1.0
NE2 G:HIS87 2.7 69.7 1.0
C1D G:HEM201 2.9 71.1 1.0
C1B G:HEM201 3.0 67.6 1.0
C4D G:HEM201 3.0 71.5 1.0
C4C G:HEM201 3.0 69.2 1.0
C4B G:HEM201 3.0 67.1 1.0
C4A G:HEM201 3.0 69.0 1.0
C1C G:HEM201 3.0 67.6 1.0
C1A G:HEM201 3.0 70.6 1.0
CE1 G:HIS87 3.3 69.7 1.0
CHD G:HEM201 3.4 71.0 1.0
CHB G:HEM201 3.4 68.6 1.0
CHC G:HEM201 3.4 67.7 1.0
CHA G:HEM201 3.4 72.0 1.0
NE2 G:HIS58 3.8 77.9 1.0
CD2 G:HIS87 3.9 70.3 1.0
C3C G:HEM201 4.2 69.3 1.0
C2C G:HEM201 4.2 68.4 1.0
C2D G:HEM201 4.2 73.0 1.0
C3D G:HEM201 4.2 73.3 1.0
C2B G:HEM201 4.2 67.2 1.0
C3A G:HEM201 4.2 70.4 1.0
C2A G:HEM201 4.2 71.3 1.0
C3B G:HEM201 4.3 67.2 1.0
CE1 G:HIS58 4.5 78.7 1.0
ND1 G:HIS87 4.6 70.7 1.0
CG2 G:VAL62 4.6 79.5 1.0
CG G:HIS87 4.9 69.4 1.0
CD1 G:LEU91 4.9 70.5 1.0
CD2 G:HIS58 5.0 78.3 1.0

Iron binding site 5 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 5 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:51.0
occ:1.00
FE J:HEM201 0.0 51.0 1.0
NA J:HEM201 1.9 52.5 1.0
NC J:HEM201 1.9 49.9 1.0
NB J:HEM201 2.0 49.5 1.0
ND J:HEM201 2.0 52.7 1.0
NE2 J:HIS92 2.0 51.3 1.0
CE1 J:HIS92 2.9 51.7 1.0
C4B J:HEM201 3.0 48.7 1.0
C1C J:HEM201 3.0 48.8 1.0
C4A J:HEM201 3.0 52.5 1.0
C1B J:HEM201 3.0 50.1 1.0
C1A J:HEM201 3.0 54.1 1.0
C4D J:HEM201 3.0 54.4 1.0
C4C J:HEM201 3.0 50.7 1.0
C1D J:HEM201 3.0 53.2 1.0
CD2 J:HIS92 3.1 52.2 1.0
CHC J:HEM201 3.3 48.8 1.0
CHB J:HEM201 3.4 51.8 1.0
CHA J:HEM201 3.4 55.3 1.0
CHD J:HEM201 3.4 52.7 1.0
ND1 J:HIS92 4.1 54.0 1.0
CG2 J:VAL67 4.1 52.8 1.0
CG J:HIS92 4.2 52.3 1.0
C3A J:HEM201 4.2 54.5 1.0
C2A J:HEM201 4.2 55.4 1.0
C2C J:HEM201 4.2 49.2 1.0
C2B J:HEM201 4.2 49.5 1.0
C3C J:HEM201 4.2 50.3 1.0
C3B J:HEM201 4.3 48.8 1.0
C3D J:HEM201 4.3 56.0 1.0
C2D J:HEM201 4.3 55.2 1.0
CE1 J:HIS63 4.3 55.1 1.0
NE2 J:HIS63 4.5 56.3 1.0

Iron binding site 6 out of 6 in 5x2s

Go back to Iron Binding Sites List in 5x2s
Iron binding site 6 out of 6 in the Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Direct Observation of Conformational Population Shifts in Hemoglobin: Crystal Structure of Half-Liganded Hemoglobin After Adding 4 Mm Bezafibrate pH 6.5. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe201

b:61.4
occ:1.00
FE K:HEM201 0.0 61.4 1.0
ND K:HEM201 1.9 62.5 1.0
NB K:HEM201 1.9 60.4 1.0
NC K:HEM201 2.0 60.5 1.0
NA K:HEM201 2.0 62.6 1.0
C1D K:HEM201 2.9 62.8 1.0
C4B K:HEM201 3.0 60.1 1.0
C4D K:HEM201 3.0 63.8 1.0
C1B K:HEM201 3.0 61.1 1.0
C4C K:HEM201 3.0 61.0 1.0
NE2 K:HIS87 3.0 58.9 1.0
C1C K:HEM201 3.0 59.8 1.0
C4A K:HEM201 3.0 62.6 1.0
C1A K:HEM201 3.0 63.8 1.0
CE1 K:HIS87 3.3 59.1 1.0
CHD K:HEM201 3.3 62.5 1.0
CHC K:HEM201 3.4 60.2 1.0
CHB K:HEM201 3.4 62.3 1.0
CHA K:HEM201 3.4 64.7 1.0
NE2 K:HIS58 4.1 72.8 1.0
CE1 K:HIS58 4.2 73.1 1.0
C3C K:HEM201 4.2 60.7 1.0
C2D K:HEM201 4.2 64.4 1.0
C3D K:HEM201 4.2 65.1 1.0
C2C K:HEM201 4.2 60.1 1.0
C2B K:HEM201 4.2 60.8 1.0
C3B K:HEM201 4.2 60.5 1.0
C2A K:HEM201 4.3 64.8 1.0
C3A K:HEM201 4.3 64.1 1.0
CD2 K:HIS87 4.3 59.4 1.0
CD1 K:LEU91 4.4 65.7 1.0
ND1 K:HIS87 4.6 60.7 1.0
CG2 K:VAL62 4.7 66.7 1.0

Reference:

N.Shibayama, M.Ohki, J.R.H.Tame, S.Y.Park. Direct Observation of Conformational Population Shifts in Crystalline Human Hemoglobin. J. Biol. Chem. V. 292 18258 2017.
ISSN: ESSN 1083-351X
PubMed: 28931607
DOI: 10.1074/JBC.M117.781146
Page generated: Tue Aug 6 11:31:17 2024

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