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Iron in PDB 7vle: Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation

Protein crystallography data

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation, PDB code: 7vle was solved by N.Numoto, S.Onoda, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.87 / 2.30
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 109.644, 109.644, 195.496, 90, 90, 120
R / Rfree (%) 20 / 24.7

Iron Binding Sites:

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation (pdb code 7vle). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 8 binding sites of Iron where determined in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation, PDB code: 7vle:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7vle

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Iron binding site 1 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:32.9
occ:1.00
FE A:HEM200 0.0 32.9 1.0
O1 A:OXY201 1.8 32.5 0.3
NE2 A:HIS94 2.0 35.1 1.0
ND A:HEM200 2.1 31.6 1.0
NC A:HEM200 2.1 32.4 1.0
NA A:HEM200 2.1 31.2 1.0
NB A:HEM200 2.1 32.3 1.0
O2 A:OXY201 2.8 33.1 0.3
CD2 A:HIS94 3.0 30.5 1.0
CE1 A:HIS94 3.0 31.8 1.0
C4C A:HEM200 3.1 29.3 1.0
C1D A:HEM200 3.1 38.7 1.0
C4D A:HEM200 3.1 32.9 1.0
C1A A:HEM200 3.1 28.1 1.0
C4A A:HEM200 3.1 31.1 1.0
C1C A:HEM200 3.1 31.8 1.0
C1B A:HEM200 3.1 32.0 1.0
C4B A:HEM200 3.1 31.1 1.0
CHD A:HEM200 3.4 33.7 1.0
CHA A:HEM200 3.4 35.2 1.0
CHB A:HEM200 3.5 35.2 1.0
CHC A:HEM200 3.5 32.1 1.0
ND1 A:HIS94 4.2 30.0 1.0
CG A:HIS94 4.2 38.5 1.0
C3D A:HEM200 4.3 35.9 1.0
C3C A:HEM200 4.3 32.4 1.0
C2D A:HEM200 4.3 34.3 1.0
C2A A:HEM200 4.3 33.3 1.0
C3A A:HEM200 4.3 30.4 1.0
C2C A:HEM200 4.3 33.6 1.0
C2B A:HEM200 4.3 36.2 1.0
C3B A:HEM200 4.3 32.0 1.0
CG2 A:VAL66 4.6 31.9 1.0
NH1 A:ARG97 4.7 35.0 0.5
CE1 A:HIS62 4.9 34.9 1.0

Iron binding site 2 out of 8 in 7vle

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Iron binding site 2 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:44.3
occ:1.00
FE B:HEM201 0.0 44.3 1.0
O1 B:OXY202 1.8 46.4 0.6
NC B:HEM201 2.0 42.8 1.0
ND B:HEM201 2.1 42.8 1.0
NE2 B:HIS95 2.1 47.2 1.0
NA B:HEM201 2.1 43.8 1.0
NB B:HEM201 2.1 40.4 1.0
O2 B:OXY202 2.8 41.6 0.6
CD2 B:HIS95 3.0 39.5 1.0
C4C B:HEM201 3.0 44.0 1.0
C1C B:HEM201 3.1 43.2 1.0
C1D B:HEM201 3.1 43.2 1.0
C4D B:HEM201 3.1 44.7 1.0
C1A B:HEM201 3.1 41.4 1.0
C4A B:HEM201 3.1 43.0 1.0
C1B B:HEM201 3.1 40.3 1.0
C4B B:HEM201 3.1 39.0 1.0
CE1 B:HIS95 3.1 48.4 1.0
CHD B:HEM201 3.4 46.6 1.0
CHC B:HEM201 3.4 47.3 1.0
CHA B:HEM201 3.4 42.3 1.0
CHB B:HEM201 3.5 33.9 1.0
CG B:HIS95 4.2 56.4 1.0
ND1 B:HIS95 4.2 51.8 1.0
C3C B:HEM201 4.3 44.0 1.0
C2C B:HEM201 4.3 47.2 1.0
C2D B:HEM201 4.3 44.4 1.0
C3A B:HEM201 4.3 42.9 1.0
C2A B:HEM201 4.3 41.1 1.0
C3D B:HEM201 4.3 44.6 1.0
C2B B:HEM201 4.3 42.8 1.0
C3B B:HEM201 4.3 39.3 1.0
CG2 B:VAL67 4.6 37.8 1.0
CE1 B:HIS63 4.8 47.7 1.0

Iron binding site 3 out of 8 in 7vle

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Iron binding site 3 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:47.5
occ:1.00
FE C:HEM200 0.0 47.5 1.0
O1 C:OXY201 1.8 43.6 0.3
NB C:HEM200 2.0 46.6 1.0
NC C:HEM200 2.0 47.8 1.0
NE2 C:HIS99 2.0 46.0 1.0
NA C:HEM200 2.1 46.3 1.0
ND C:HEM200 2.1 49.4 1.0
O2 C:OXY201 2.8 44.0 0.3
CD2 C:HIS99 2.9 52.0 1.0
C1B C:HEM200 3.0 44.6 1.0
C4C C:HEM200 3.1 52.0 1.0
C4A C:HEM200 3.1 47.1 1.0
C1C C:HEM200 3.1 48.9 1.0
C4B C:HEM200 3.1 43.6 1.0
C1D C:HEM200 3.1 48.8 1.0
CE1 C:HIS99 3.1 46.2 1.0
C1A C:HEM200 3.1 48.3 1.0
C4D C:HEM200 3.1 48.4 1.0
CHB C:HEM200 3.4 43.3 1.0
CHD C:HEM200 3.4 49.9 1.0
CHC C:HEM200 3.4 46.3 1.0
CHA C:HEM200 3.5 47.3 1.0
CG C:HIS99 4.1 53.3 1.0
ND1 C:HIS99 4.1 46.7 1.0
C2B C:HEM200 4.3 48.6 1.0
C2C C:HEM200 4.3 46.7 1.0
C3C C:HEM200 4.3 52.1 1.0
C3B C:HEM200 4.3 44.5 1.0
C3A C:HEM200 4.3 51.3 1.0
C2A C:HEM200 4.3 48.8 1.0
C2D C:HEM200 4.3 55.1 1.0
C3D C:HEM200 4.4 57.0 1.0
CG2 C:VAL71 4.5 43.1 1.0
CE1 C:HIS67 4.8 43.0 1.0

Iron binding site 4 out of 8 in 7vle

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Iron binding site 4 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:41.2
occ:1.00
FE D:HEM201 0.0 41.2 1.0
O1 D:OXY202 1.8 41.0 0.9
ND D:HEM201 2.0 51.2 1.0
NB D:HEM201 2.0 44.8 1.0
NA D:HEM201 2.0 46.8 1.0
NC D:HEM201 2.0 48.0 1.0
NE2 D:HIS99 2.1 38.6 1.0
O2 D:OXY202 2.8 46.3 0.9
C1D D:HEM201 3.0 50.0 1.0
C4D D:HEM201 3.0 47.8 1.0
C4C D:HEM201 3.0 51.4 1.0
C1B D:HEM201 3.0 41.1 1.0
C4A D:HEM201 3.0 44.3 1.0
C4B D:HEM201 3.0 41.5 1.0
C1A D:HEM201 3.0 45.5 1.0
CE1 D:HIS99 3.0 43.6 1.0
C1C D:HEM201 3.0 52.0 1.0
CD2 D:HIS99 3.1 42.7 1.0
CHD D:HEM201 3.3 50.8 1.0
CHB D:HEM201 3.4 41.5 1.0
CHA D:HEM201 3.4 42.1 1.0
CHC D:HEM201 3.4 47.1 1.0
ND1 D:HIS99 4.2 44.3 1.0
C2D D:HEM201 4.2 47.6 1.0
CG D:HIS99 4.2 49.0 1.0
C3D D:HEM201 4.2 48.3 1.0
C3C D:HEM201 4.2 51.3 1.0
C2B D:HEM201 4.2 44.7 1.0
C3B D:HEM201 4.2 43.6 1.0
C3A D:HEM201 4.2 43.3 1.0
C2C D:HEM201 4.2 48.1 1.0
C2A D:HEM201 4.2 48.1 1.0
CG2 D:VAL71 4.6 37.2 1.0
CZ D:PHE110 4.7 51.5 1.0

Iron binding site 5 out of 8 in 7vle

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Iron binding site 5 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:37.1
occ:1.00
FE E:HEM200 0.0 37.1 1.0
O1 E:OXY201 1.8 34.9 0.6
NC E:HEM200 2.0 36.6 1.0
NE2 E:HIS94 2.1 34.7 1.0
ND E:HEM200 2.1 34.1 1.0
NA E:HEM200 2.1 33.9 1.0
NB E:HEM200 2.1 35.4 1.0
O2 E:OXY201 2.8 36.4 0.6
CE1 E:HIS94 3.0 34.1 1.0
C4C E:HEM200 3.0 35.7 1.0
C1D E:HEM200 3.1 38.9 1.0
C1B E:HEM200 3.1 35.5 1.0
C4A E:HEM200 3.1 33.1 1.0
C1C E:HEM200 3.1 35.7 1.0
C4D E:HEM200 3.1 39.2 1.0
C1A E:HEM200 3.1 34.1 1.0
CD2 E:HIS94 3.1 31.5 1.0
C4B E:HEM200 3.1 32.9 1.0
CHD E:HEM200 3.4 36.0 1.0
CHB E:HEM200 3.4 34.0 1.0
CHA E:HEM200 3.5 39.6 1.0
CHC E:HEM200 3.5 36.8 1.0
ND1 E:HIS94 4.1 35.5 1.0
CG E:HIS94 4.2 40.1 1.0
C3C E:HEM200 4.3 37.5 1.0
C2C E:HEM200 4.3 36.2 1.0
C2B E:HEM200 4.3 35.3 1.0
C3A E:HEM200 4.3 31.2 1.0
C2D E:HEM200 4.3 40.9 1.0
C2A E:HEM200 4.3 33.8 1.0
C3D E:HEM200 4.3 39.6 1.0
C3B E:HEM200 4.3 38.9 1.0
CG2 E:VAL66 4.8 35.3 1.0
CE1 E:HIS62 4.9 41.6 1.0

Iron binding site 6 out of 8 in 7vle

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Iron binding site 6 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:42.1
occ:1.00
FE F:HEM201 0.0 42.1 1.0
O1 F:OXY202 1.8 38.8 0.7
NC F:HEM201 2.0 36.1 1.0
NB F:HEM201 2.0 37.2 1.0
NE2 F:HIS95 2.1 41.2 1.0
NA F:HEM201 2.1 34.7 1.0
ND F:HEM201 2.1 40.5 1.0
O2 F:OXY202 2.8 39.8 0.7
CE1 F:HIS95 3.0 42.8 1.0
C1C F:HEM201 3.0 39.0 1.0
C4C F:HEM201 3.0 39.3 1.0
C1B F:HEM201 3.1 34.7 1.0
C4B F:HEM201 3.1 40.4 1.0
CD2 F:HIS95 3.1 45.8 1.0
C4A F:HEM201 3.1 34.7 1.0
C1D F:HEM201 3.1 38.4 1.0
C1A F:HEM201 3.1 37.7 1.0
C4D F:HEM201 3.1 41.5 1.0
CHC F:HEM201 3.4 40.1 1.0
CHD F:HEM201 3.4 41.5 1.0
CHB F:HEM201 3.4 37.7 1.0
CHA F:HEM201 3.5 42.6 1.0
ND1 F:HIS95 4.1 43.9 1.0
CG F:HIS95 4.2 48.3 1.0
C2C F:HEM201 4.2 39.8 1.0
C3C F:HEM201 4.2 38.8 1.0
C2B F:HEM201 4.3 34.9 1.0
C3B F:HEM201 4.3 36.6 1.0
C3A F:HEM201 4.3 34.8 1.0
C2D F:HEM201 4.3 41.8 1.0
C2A F:HEM201 4.4 33.8 1.0
C3D F:HEM201 4.4 37.9 1.0
CE1 F:HIS63 4.8 41.0 1.0
CG2 F:VAL67 4.8 38.1 1.0

Iron binding site 7 out of 8 in 7vle

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Iron binding site 7 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe200

b:48.1
occ:1.00
FE G:HEM200 0.0 48.1 1.0
O1 G:OXY201 1.8 47.1 0.8
NB G:HEM200 1.9 46.9 1.0
NA G:HEM200 2.0 47.1 1.0
NC G:HEM200 2.0 48.3 1.0
NE2 G:HIS99 2.0 50.0 1.0
ND G:HEM200 2.0 48.9 1.0
O2 G:OXY201 2.8 46.5 0.8
C1B G:HEM200 2.9 37.1 1.0
C4B G:HEM200 2.9 44.8 1.0
CE1 G:HIS99 2.9 46.4 1.0
C4A G:HEM200 3.0 42.1 1.0
C1A G:HEM200 3.0 45.9 1.0
C1C G:HEM200 3.0 50.0 1.0
C4D G:HEM200 3.1 50.3 1.0
CD2 G:HIS99 3.1 52.3 1.0
C1D G:HEM200 3.1 48.2 1.0
C4C G:HEM200 3.1 46.0 1.0
CHB G:HEM200 3.3 36.9 1.0
CHC G:HEM200 3.4 43.1 1.0
CHA G:HEM200 3.4 47.9 1.0
CHD G:HEM200 3.5 43.3 1.0
ND1 G:HIS99 4.1 48.6 1.0
C3B G:HEM200 4.1 40.1 1.0
C2B G:HEM200 4.1 44.2 1.0
CG G:HIS99 4.2 51.2 1.0
C3A G:HEM200 4.2 45.9 1.0
C2A G:HEM200 4.2 43.0 1.0
C2C G:HEM200 4.3 39.6 1.0
C2D G:HEM200 4.3 47.0 1.0
C3D G:HEM200 4.3 42.7 1.0
C3C G:HEM200 4.3 45.0 1.0
CE1 G:HIS67 4.4 40.7 1.0
CG2 G:VAL71 4.5 43.2 1.0
NE2 G:HIS67 4.6 43.8 1.0

Iron binding site 8 out of 8 in 7vle

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Iron binding site 8 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Oxy-Deoxy Intermediate of V2 Hemoglobin at 55% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:32.3
occ:1.00
FE H:HEM201 0.0 32.3 1.0
O1 H:OXY202 1.8 33.0 0.2
NC H:HEM201 2.0 37.3 1.0
NE2 H:HIS99 2.0 35.9 1.0
NA H:HEM201 2.1 33.7 1.0
NB H:HEM201 2.1 32.4 1.0
ND H:HEM201 2.1 32.4 1.0
O2 H:OXY202 2.8 33.4 0.2
CE1 H:HIS99 2.9 36.0 1.0
C4C H:HEM201 3.0 36.4 1.0
C1B H:HEM201 3.1 34.0 1.0
C4A H:HEM201 3.1 35.5 1.0
C1D H:HEM201 3.1 38.0 1.0
C1C H:HEM201 3.1 36.6 1.0
C1A H:HEM201 3.1 37.7 1.0
C4B H:HEM201 3.1 34.8 1.0
C4D H:HEM201 3.1 36.2 1.0
CD2 H:HIS99 3.1 38.2 1.0
CHD H:HEM201 3.4 37.3 1.0
CHB H:HEM201 3.4 31.9 1.0
CHC H:HEM201 3.5 37.0 1.0
CHA H:HEM201 3.5 33.0 1.0
ND1 H:HIS99 4.1 35.5 1.0
CG H:HIS99 4.2 41.4 1.0
C3C H:HEM201 4.3 38.5 1.0
C3A H:HEM201 4.3 32.6 1.0
C2B H:HEM201 4.3 37.4 1.0
C2C H:HEM201 4.3 33.6 1.0
C2A H:HEM201 4.3 35.4 1.0
C2D H:HEM201 4.3 43.5 1.0
C3B H:HEM201 4.3 36.1 1.0
C3D H:HEM201 4.3 41.7 1.0
CG2 H:VAL71 4.5 27.8 1.0
CE1 H:HIS67 4.9 32.1 1.0
CZ H:PHE110 4.9 37.0 1.0

Reference:

N.Numoto, S.Onoda, Y.Kawano, H.Okumura, S.Baba, Y.Fukumori, K.Miki, N.Ito. Structures of Oxygen Dissociation Intermediates of 400 kDa V2 Hemoglobin Provide Coarse Snapshots of the Protein Allostery. Biophys Physicobio. V. 19 1 2022.
ISSN: ESSN 2189-4779
PubMed: 35797404
DOI: 10.2142/BIOPHYSICO.BPPB-V19.0019
Page generated: Fri Aug 9 05:32:05 2024

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