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Iron in PDB 4n7p: Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.

Protein crystallography data

The structure of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution., PDB code: 4n7p was solved by K.Sugiyama, N.Shibayama, S.Y.Park, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.81
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 228.331, 55.531, 139.681, 90.00, 103.08, 90.00
R / Rfree (%) 25.9 / 28.7

Other elements in 4n7p:

The structure of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. also contains other interesting chemical elements:

Nickel (Ni) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. (pdb code 4n7p). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution., PDB code: 4n7p:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 1 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:53.5
occ:1.00
FE B:HEM201 0.0 53.5 1.0
NC B:HEM201 2.0 48.2 1.0
NA B:HEM201 2.0 52.4 1.0
NB B:HEM201 2.1 52.6 1.0
ND B:HEM201 2.1 51.8 1.0
NE2 B:HIS92 2.2 40.5 1.0
CD2 B:HIS92 2.9 46.3 1.0
C4C B:HEM201 3.0 47.5 1.0
C1B B:HEM201 3.1 52.9 1.0
C4A B:HEM201 3.1 54.3 1.0
C1C B:HEM201 3.1 49.6 1.0
C1A B:HEM201 3.1 54.5 1.0
C1D B:HEM201 3.1 53.1 1.0
C4B B:HEM201 3.1 53.8 1.0
C4D B:HEM201 3.1 53.8 1.0
CE1 B:HIS92 3.3 47.0 1.0
CHB B:HEM201 3.4 53.6 1.0
CHD B:HEM201 3.4 49.1 1.0
CHA B:HEM201 3.4 54.1 1.0
CHC B:HEM201 3.5 51.5 1.0
CG B:HIS92 4.2 50.0 1.0
NE2 B:HIS63 4.2 78.2 1.0
C3C B:HEM201 4.3 45.9 1.0
C2C B:HEM201 4.3 45.6 1.0
C3A B:HEM201 4.3 53.2 1.0
C2A B:HEM201 4.3 54.4 1.0
ND1 B:HIS92 4.3 49.5 1.0
C2B B:HEM201 4.3 55.6 1.0
C3B B:HEM201 4.3 56.5 1.0
C2D B:HEM201 4.4 53.2 1.0
C3D B:HEM201 4.4 54.9 1.0
CG2 B:VAL67 4.8 65.0 1.0

Iron binding site 2 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 2 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:77.5
occ:1.00
FE C:HEM201 0.0 77.5 1.0
NC C:HEM201 2.0 77.6 1.0
NA C:HEM201 2.0 81.7 1.0
NB C:HEM201 2.0 77.6 1.0
ND C:HEM201 2.1 77.7 1.0
NE2 C:HIS87 2.5 82.3 1.0
C1B C:HEM201 3.0 80.0 1.0
C4C C:HEM201 3.0 75.1 1.0
C4A C:HEM201 3.1 82.3 1.0
C1C C:HEM201 3.1 76.5 1.0
C1A C:HEM201 3.1 83.7 1.0
C1D C:HEM201 3.1 78.3 1.0
C4B C:HEM201 3.1 76.6 1.0
C4D C:HEM201 3.1 80.5 1.0
CD2 C:HIS87 3.4 84.7 1.0
CHB C:HEM201 3.4 80.5 1.0
CHD C:HEM201 3.4 77.5 1.0
CHA C:HEM201 3.5 82.2 1.0
CHC C:HEM201 3.5 76.6 1.0
CE1 C:HIS87 3.6 83.3 1.0
NE2 C:HIS58 4.2 0.9 1.0
C3C C:HEM201 4.3 74.0 1.0
C2B C:HEM201 4.3 79.8 1.0
C2C C:HEM201 4.3 75.1 1.0
C3A C:HEM201 4.3 83.8 1.0
C3B C:HEM201 4.3 78.1 1.0
C2A C:HEM201 4.3 85.1 1.0
C2D C:HEM201 4.4 79.6 1.0
C3D C:HEM201 4.4 82.7 1.0
CE1 C:HIS58 4.4 0.4 1.0
CG C:HIS87 4.6 85.4 1.0
ND1 C:HIS87 4.6 84.5 1.0

Iron binding site 3 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 3 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:48.6
occ:1.00
FE F:HEM201 0.0 48.6 1.0
NC F:HEM201 2.0 47.4 1.0
NB F:HEM201 2.0 47.2 1.0
NA F:HEM201 2.1 49.9 1.0
ND F:HEM201 2.1 49.8 1.0
NE2 F:HIS92 2.1 59.5 1.0
C1B F:HEM201 3.0 47.2 1.0
C4C F:HEM201 3.1 46.8 1.0
C4A F:HEM201 3.1 49.4 1.0
C1C F:HEM201 3.1 47.4 1.0
C4B F:HEM201 3.1 48.9 1.0
C1A F:HEM201 3.1 53.1 1.0
CD2 F:HIS92 3.1 60.4 1.0
C1D F:HEM201 3.1 50.1 1.0
CE1 F:HIS92 3.1 61.4 1.0
C4D F:HEM201 3.1 53.5 1.0
CHB F:HEM201 3.4 48.6 1.0
CHD F:HEM201 3.4 47.6 1.0
CHC F:HEM201 3.5 49.1 1.0
CHA F:HEM201 3.5 52.3 1.0
ND1 F:HIS92 4.2 61.1 1.0
CG F:HIS92 4.3 61.6 1.0
C3C F:HEM201 4.3 47.3 1.0
C2B F:HEM201 4.3 47.5 1.0
C2C F:HEM201 4.3 46.8 1.0
C3A F:HEM201 4.3 51.4 1.0
C2A F:HEM201 4.3 53.5 1.0
C3B F:HEM201 4.3 48.5 1.0
C2D F:HEM201 4.4 51.2 1.0
C3D F:HEM201 4.4 56.0 1.0
NE2 F:HIS63 4.4 64.3 1.0
CG2 F:VAL67 4.5 47.2 1.0

Iron binding site 4 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 4 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe201

b:78.1
occ:1.00
FE G:HEM201 0.0 78.1 1.0
NC G:HEM201 2.0 81.5 1.0
NA G:HEM201 2.0 82.7 1.0
NB G:HEM201 2.1 81.3 1.0
ND G:HEM201 2.1 80.9 1.0
NE2 G:HIS87 2.3 69.0 1.0
CE1 G:HIS87 2.9 70.8 1.0
C4C G:HEM201 3.0 80.9 1.0
C4A G:HEM201 3.1 83.2 1.0
C1B G:HEM201 3.1 82.0 1.0
C1D G:HEM201 3.1 80.8 1.0
C1A G:HEM201 3.1 83.6 1.0
C1C G:HEM201 3.1 81.4 1.0
C4D G:HEM201 3.1 80.7 1.0
C4B G:HEM201 3.1 80.7 1.0
CHD G:HEM201 3.4 81.0 1.0
CHB G:HEM201 3.4 83.4 1.0
CHA G:HEM201 3.5 82.0 1.0
CD2 G:HIS87 3.5 71.4 1.0
CHC G:HEM201 3.5 82.8 1.0
NE2 G:HIS58 4.2 68.9 1.0
ND1 G:HIS87 4.2 72.7 1.0
C3C G:HEM201 4.3 80.9 1.0
C3A G:HEM201 4.3 84.4 1.0
C2C G:HEM201 4.3 80.3 1.0
C2A G:HEM201 4.3 85.2 1.0
C2D G:HEM201 4.3 80.6 1.0
C2B G:HEM201 4.3 82.2 1.0
C3D G:HEM201 4.4 80.4 1.0
C3B G:HEM201 4.4 81.8 1.0
CG2 G:VAL62 4.5 71.5 1.0
CG G:HIS87 4.5 72.8 1.0
CE1 G:HIS58 4.8 66.6 1.0

Iron binding site 5 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 5 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Fe201

b:0.4
occ:1.00
FE J:HEM201 0.0 0.4 1.0
NC J:HEM201 2.0 0.2 1.0
NA J:HEM201 2.1 0.6 1.0
NB J:HEM201 2.1 1.0 1.0
ND J:HEM201 2.1 0.1 1.0
NE2 J:HIS92 2.2 94.4 1.0
CE1 J:HIS92 3.0 95.2 1.0
C4C J:HEM201 3.1 0.4 1.0
C1B J:HEM201 3.1 0.1 1.0
C4A J:HEM201 3.1 0.6 1.0
C1A J:HEM201 3.1 0.1 1.0
C1D J:HEM201 3.1 0.4 1.0
C1C J:HEM201 3.1 0.4 1.0
C4D J:HEM201 3.1 0.1 1.0
CD2 J:HIS92 3.1 97.7 1.0
C4B J:HEM201 3.1 0.2 1.0
CHB J:HEM201 3.4 0.4 1.0
CHD J:HEM201 3.4 0.5 1.0
CHA J:HEM201 3.4 0.1 1.0
CHC J:HEM201 3.5 0.5 1.0
ND1 J:HIS92 4.1 97.7 1.0
CG2 J:VAL67 4.2 77.2 1.0
CG J:HIS92 4.2 99.1 1.0
NE2 J:HIS63 4.2 91.3 1.0
C3C J:HEM201 4.3 0.9 1.0
C2C J:HEM201 4.3 0.2 1.0
C3A J:HEM201 4.3 0.9 1.0
C2A J:HEM201 4.3 0.6 1.0
C2B J:HEM201 4.3 0.2 1.0
C3B J:HEM201 4.4 0.3 1.0
C2D J:HEM201 4.4 0.4 1.0
C3D J:HEM201 4.4 0.0 1.0

Iron binding site 6 out of 6 in 4n7p

Go back to Iron Binding Sites List in 4n7p
Iron binding site 6 out of 6 in the Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Capturing the Haemoglobin Allosteric Transition in A Single Crystal Form; Crystal Structure of Half-Liganded Human Haemoglobin Without Phosphate at 2.8 A Resolution. within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Fe201

b:0.0
occ:1.00
FE K:HEM201 0.0 0.0 1.0
NC K:HEM201 2.1 0.9 1.0
NA K:HEM201 2.1 0.7 1.0
NB K:HEM201 2.1 0.3 1.0
ND K:HEM201 2.1 0.3 1.0
NE2 K:HIS87 2.4 96.2 1.0
C1B K:HEM201 3.1 0.0 1.0
C4C K:HEM201 3.1 0.1 1.0
C4A K:HEM201 3.1 0.1 1.0
C1D K:HEM201 3.1 0.8 1.0
C1A K:HEM201 3.1 0.8 1.0
C1C K:HEM201 3.1 0.7 1.0
C4D K:HEM201 3.1 0.2 1.0
C4B K:HEM201 3.1 0.7 1.0
CE1 K:HIS87 3.1 97.8 1.0
CHB K:HEM201 3.4 0.4 1.0
CHD K:HEM201 3.4 0.1 1.0
CHA K:HEM201 3.5 0.4 1.0
CHC K:HEM201 3.5 0.2 1.0
CD2 K:HIS87 3.6 98.1 1.0
CE1 K:HIS58 4.0 1.0 1.0
NE2 K:HIS58 4.1 0.9 1.0
C3A K:HEM201 4.3 0.0 1.0
C2D K:HEM201 4.3 0.1 1.0
C2A K:HEM201 4.3 0.2 1.0
C2B K:HEM201 4.3 0.6 1.0
C3C K:HEM201 4.3 0.6 1.0
C2C K:HEM201 4.4 0.3 1.0
C3B K:HEM201 4.4 0.5 1.0
C3D K:HEM201 4.4 0.3 1.0
ND1 K:HIS87 4.4 98.5 1.0
CG K:HIS87 4.6 98.7 1.0

Reference:

N.Shibayama, K.Sugiyama, J.R.Tame, S.Y.Park. Capturing the Hemoglobin Allosteric Transition in A Single Crystal Form J.Am.Chem.Soc. V. 136 5097 2014.
ISSN: ISSN 0002-7863
PubMed: 24635037
DOI: 10.1021/JA500380E
Page generated: Mon Aug 5 07:16:30 2024

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