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Iron in PDB 7vlf: Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% Oxygen Saturation

Protein crystallography data

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% Oxygen Saturation, PDB code: 7vlf 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) 47.56 / 2.40
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 109.009, 109.009, 194.68, 90, 90, 120
R / Rfree (%) 24.5 / 27.4

Other elements in 7vlf:

The structure of Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% Oxygen Saturation also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% Oxygen Saturation (pdb code 7vlf). 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 26% Oxygen Saturation, PDB code: 7vlf:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 7vlf

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Iron binding site 1 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe200

b:34.6
occ:1.00
FE A:HEM200 0.0 34.6 1.0
NA A:HEM200 2.0 31.0 1.0
ND A:HEM200 2.1 34.2 1.0
NC A:HEM200 2.1 38.1 1.0
NB A:HEM200 2.1 38.9 1.0
NE2 A:HIS94 2.2 33.1 1.0
CE1 A:HIS94 2.9 35.3 1.0
C1A A:HEM200 3.0 38.9 1.0
C4A A:HEM200 3.1 38.3 1.0
C4D A:HEM200 3.1 35.6 1.0
C1D A:HEM200 3.1 39.1 1.0
C1C A:HEM200 3.1 37.4 1.0
C4C A:HEM200 3.1 41.7 1.0
C4B A:HEM200 3.1 33.6 1.0
C1B A:HEM200 3.1 40.4 1.0
CD2 A:HIS94 3.4 32.6 1.0
CHA A:HEM200 3.4 36.4 1.0
CHD A:HEM200 3.4 44.1 1.0
CHB A:HEM200 3.5 39.6 1.0
CHC A:HEM200 3.5 36.5 1.0
CG2 A:VAL66 4.1 37.3 1.0
ND1 A:HIS94 4.1 39.2 1.0
C2A A:HEM200 4.3 44.7 1.0
C3A A:HEM200 4.3 36.6 1.0
C2C A:HEM200 4.3 38.7 1.0
C2D A:HEM200 4.3 37.2 1.0
C3D A:HEM200 4.3 38.0 1.0
C3C A:HEM200 4.3 40.0 1.0
C2B A:HEM200 4.3 34.0 1.0
C3B A:HEM200 4.3 33.3 1.0
CG A:HIS94 4.4 36.9 1.0
NH1 A:ARG97 4.7 35.9 1.0
CE1 A:HIS62 4.8 44.8 1.0
CG1 A:VAL66 4.9 36.5 1.0

Iron binding site 2 out of 8 in 7vlf

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Iron binding site 2 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:57.0
occ:1.00
FE B:HEM201 0.0 57.0 1.0
ND B:HEM201 1.9 57.7 1.0
NA B:HEM201 2.0 58.4 1.0
NB B:HEM201 2.0 57.8 1.0
NC B:HEM201 2.1 57.2 1.0
NE2 B:HIS95 2.2 57.6 1.0
C4D B:HEM201 2.9 58.5 1.0
C1D B:HEM201 3.0 58.0 1.0
C1A B:HEM201 3.0 58.3 1.0
C4C B:HEM201 3.0 57.0 1.0
C4A B:HEM201 3.0 57.6 1.0
C4B B:HEM201 3.1 56.8 1.0
C1B B:HEM201 3.1 57.1 1.0
C1C B:HEM201 3.1 57.1 1.0
CE1 B:HIS95 3.1 60.0 1.0
CD2 B:HIS95 3.1 57.2 1.0
CHA B:HEM201 3.3 58.8 1.0
CHD B:HEM201 3.4 57.7 1.0
CHC B:HEM201 3.5 56.9 1.0
CHB B:HEM201 3.5 57.6 1.0
CG2 B:VAL67 4.0 57.5 1.0
C3D B:HEM201 4.2 58.7 1.0
C2D B:HEM201 4.2 58.5 1.0
ND1 B:HIS95 4.2 60.6 1.0
C2A B:HEM201 4.2 59.4 1.0
C3A B:HEM201 4.2 58.7 1.0
CG B:HIS95 4.3 60.1 1.0
C3C B:HEM201 4.3 57.1 1.0
C2C B:HEM201 4.3 56.9 1.0
C3B B:HEM201 4.3 57.1 1.0
C2B B:HEM201 4.3 57.2 1.0
CE1 B:HIS63 4.7 59.9 1.0
CE1 B:PHE47 4.8 58.7 1.0
CG1 B:VAL67 4.9 55.9 1.0

Iron binding site 3 out of 8 in 7vlf

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Iron binding site 3 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe200

b:47.1
occ:1.00
FE C:HEM200 0.0 47.1 1.0
O1 C:OXY201 1.8 50.1 0.4
NC C:HEM200 2.0 45.7 1.0
ND C:HEM200 2.1 51.0 1.0
NA C:HEM200 2.1 49.0 1.0
NB C:HEM200 2.1 56.2 1.0
NE2 C:HIS99 2.2 52.7 1.0
O2 C:OXY201 2.8 51.3 0.4
C1D C:HEM200 3.1 52.5 1.0
C4C C:HEM200 3.1 47.8 1.0
C1C C:HEM200 3.1 54.3 1.0
C4D C:HEM200 3.1 51.6 1.0
C1A C:HEM200 3.1 54.0 1.0
C4B C:HEM200 3.1 54.4 1.0
C4A C:HEM200 3.1 48.5 1.0
C1B C:HEM200 3.1 53.4 1.0
CE1 C:HIS99 3.1 56.0 1.0
CD2 C:HIS99 3.2 56.0 1.0
CHD C:HEM200 3.4 51.5 1.0
CHA C:HEM200 3.4 52.7 1.0
CHC C:HEM200 3.4 54.1 1.0
CHB C:HEM200 3.5 51.2 1.0
ND1 C:HIS99 4.3 67.0 1.0
C2C C:HEM200 4.3 52.7 1.0
C3C C:HEM200 4.3 52.5 1.0
C2D C:HEM200 4.3 52.9 1.0
CG C:HIS99 4.3 63.7 1.0
C3D C:HEM200 4.3 48.1 1.0
C2A C:HEM200 4.3 51.6 1.0
C3A C:HEM200 4.3 49.5 1.0
C3B C:HEM200 4.3 52.5 1.0
C2B C:HEM200 4.3 50.4 1.0
CG2 C:VAL71 4.4 49.8 1.0
CG1 C:VAL71 4.7 46.6 1.0
CE1 C:HIS67 5.0 52.2 1.0

Iron binding site 4 out of 8 in 7vlf

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Iron binding site 4 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:51.5
occ:1.00
FE D:HEM201 0.0 51.5 1.0
O1 D:OXY202 1.8 51.2 0.3
NC D:HEM201 2.0 50.1 1.0
NB D:HEM201 2.1 56.5 1.0
ND D:HEM201 2.1 55.8 1.0
NA D:HEM201 2.1 52.6 1.0
NE2 D:HIS99 2.2 48.7 1.0
O2 D:OXY202 2.8 51.7 0.3
C4C D:HEM201 3.0 56.5 1.0
C1C D:HEM201 3.0 55.8 1.0
C4B D:HEM201 3.1 55.9 1.0
C1D D:HEM201 3.1 57.1 1.0
C1B D:HEM201 3.1 53.1 1.0
C4D D:HEM201 3.1 55.0 1.0
C1A D:HEM201 3.1 54.3 1.0
C4A D:HEM201 3.1 52.6 1.0
CD2 D:HIS99 3.1 54.2 1.0
CE1 D:HIS99 3.2 51.8 1.0
CHD D:HEM201 3.4 56.7 1.0
CHC D:HEM201 3.4 56.6 1.0
CHA D:HEM201 3.5 50.5 1.0
CHB D:HEM201 3.5 52.4 1.0
C3C D:HEM201 4.3 61.2 1.0
C2C D:HEM201 4.3 59.4 1.0
CG D:HIS99 4.3 58.0 1.0
ND1 D:HIS99 4.3 54.1 1.0
C3B D:HEM201 4.3 56.2 1.0
CG2 D:VAL71 4.3 46.0 1.0
C2B D:HEM201 4.3 53.7 1.0
C2D D:HEM201 4.3 60.7 1.0
C2A D:HEM201 4.3 51.6 1.0
C3A D:HEM201 4.3 47.1 1.0
C3D D:HEM201 4.3 65.1 1.0
CG1 D:VAL71 4.9 59.1 1.0
CZ D:PHE110 4.9 59.1 1.0

Iron binding site 5 out of 8 in 7vlf

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Iron binding site 5 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe200

b:53.1
occ:1.00
FE E:HEM200 0.0 53.1 1.0
NA E:HEM200 2.0 42.5 1.0
NC E:HEM200 2.1 48.1 1.0
NB E:HEM200 2.1 42.8 1.0
ND E:HEM200 2.1 46.0 1.0
NE2 E:HIS94 2.2 41.6 1.0
CE1 E:HIS94 2.7 42.1 1.0
C4C E:HEM200 3.1 47.1 1.0
C1A E:HEM200 3.1 47.3 1.0
C4A E:HEM200 3.1 48.3 1.0
C1B E:HEM200 3.1 44.2 1.0
C1D E:HEM200 3.1 52.3 1.0
C4B E:HEM200 3.1 39.5 1.0
C1C E:HEM200 3.1 45.3 1.0
C4D E:HEM200 3.1 48.0 1.0
CHD E:HEM200 3.4 50.5 1.0
CHB E:HEM200 3.4 46.0 1.0
CHA E:HEM200 3.4 51.9 1.0
CHC E:HEM200 3.5 43.3 1.0
CD2 E:HIS94 3.5 41.0 1.0
ND1 E:HIS94 4.0 46.1 1.0
C3A E:HEM200 4.3 46.2 1.0
C2A E:HEM200 4.3 43.1 1.0
C2B E:HEM200 4.3 43.5 1.0
C3C E:HEM200 4.3 48.3 1.0
C3B E:HEM200 4.3 44.6 1.0
C2C E:HEM200 4.3 47.9 1.0
C2D E:HEM200 4.3 51.0 1.0
CG2 E:VAL66 4.3 44.0 1.0
C3D E:HEM200 4.3 46.3 1.0
CG E:HIS94 4.4 48.3 1.0
CE1 E:HIS62 4.8 51.6 1.0
NH1 E:ARG97 4.9 50.9 1.0

Iron binding site 6 out of 8 in 7vlf

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Iron binding site 6 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe201

b:51.1
occ:1.00
FE F:HEM201 0.0 51.1 1.0
O1 F:OXY202 1.8 51.0 0.4
NC F:HEM201 2.0 48.8 1.0
NB F:HEM201 2.1 48.4 1.0
ND F:HEM201 2.1 53.9 1.0
NA F:HEM201 2.1 49.2 1.0
NE2 F:HIS95 2.2 53.2 1.0
O2 F:OXY202 2.8 51.6 0.4
C4C F:HEM201 3.0 51.0 1.0
C1C F:HEM201 3.0 53.2 1.0
C4B F:HEM201 3.1 45.0 1.0
C1B F:HEM201 3.1 51.3 1.0
C1D F:HEM201 3.1 51.6 1.0
CD2 F:HIS95 3.1 59.5 1.0
C4D F:HEM201 3.1 56.3 1.0
C4A F:HEM201 3.1 53.7 1.0
C1A F:HEM201 3.1 53.4 1.0
CE1 F:HIS95 3.2 56.5 1.0
CHC F:HEM201 3.4 49.7 1.0
CHD F:HEM201 3.4 51.4 1.0
CHA F:HEM201 3.5 56.8 1.0
CHB F:HEM201 3.5 51.7 1.0
C2C F:HEM201 4.2 48.1 1.0
C3C F:HEM201 4.2 46.0 1.0
C3B F:HEM201 4.3 45.5 1.0
C2B F:HEM201 4.3 50.2 1.0
CG F:HIS95 4.3 59.1 1.0
ND1 F:HIS95 4.3 59.9 1.0
C3A F:HEM201 4.3 63.0 1.0
C2A F:HEM201 4.3 62.8 1.0
C2D F:HEM201 4.3 53.0 1.0
C3D F:HEM201 4.3 53.6 1.0
CG2 F:VAL67 4.4 51.0 1.0
CE1 F:HIS63 4.9 54.6 1.0
CG1 F:VAL67 4.9 43.9 1.0

Iron binding site 7 out of 8 in 7vlf

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Iron binding site 7 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Fe200

b:57.7
occ:1.00
FE G:HEM200 0.0 57.7 1.0
O1 G:OXY201 1.8 55.4 1.0
NC G:HEM200 2.0 55.4 1.0
NB G:HEM200 2.1 55.8 1.0
ND G:HEM200 2.1 57.8 1.0
NA G:HEM200 2.1 59.1 1.0
NE2 G:HIS99 2.2 59.8 1.0
O2 G:OXY201 2.8 57.1 1.0
C1C G:HEM200 3.1 58.2 1.0
C4C G:HEM200 3.1 56.0 1.0
C1D G:HEM200 3.1 56.9 1.0
C1B G:HEM200 3.1 57.4 1.0
C4B G:HEM200 3.1 56.0 1.0
C4D G:HEM200 3.1 61.4 1.0
C1A G:HEM200 3.1 60.0 1.0
C4A G:HEM200 3.1 57.1 1.0
CE1 G:HIS99 3.1 61.1 1.0
CD2 G:HIS99 3.2 59.7 1.0
CHD G:HEM200 3.4 57.7 1.0
CHC G:HEM200 3.4 59.0 1.0
CHA G:HEM200 3.5 61.7 1.0
CHB G:HEM200 3.5 57.0 1.0
ND1 G:HIS99 4.2 63.6 1.0
C2C G:HEM200 4.3 56.2 1.0
C3C G:HEM200 4.3 55.9 1.0
C2B G:HEM200 4.3 57.1 1.0
C2D G:HEM200 4.3 56.3 1.0
C3B G:HEM200 4.3 57.1 1.0
CG G:HIS99 4.3 62.9 1.0
C3D G:HEM200 4.3 58.7 1.0
C2A G:HEM200 4.3 58.7 1.0
C3A G:HEM200 4.3 57.5 1.0
CG2 G:VAL71 4.6 53.8 1.0
CG1 G:VAL71 4.7 54.7 1.0

Iron binding site 8 out of 8 in 7vlf

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Iron binding site 8 out of 8 in the Oxy-Deoxy Intermediate of V2 Hemoglobin at 26% 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 26% Oxygen Saturation within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Fe201

b:49.4
occ:1.00
FE H:HEM201 0.0 49.4 1.0
NC H:HEM201 2.0 51.0 1.0
NB H:HEM201 2.1 45.8 1.0
NA H:HEM201 2.1 50.5 1.0
ND H:HEM201 2.1 51.3 1.0
NE2 H:HIS99 2.2 48.2 1.0
CE1 H:HIS99 3.0 48.8 1.0
C4C H:HEM201 3.0 51.2 1.0
C1C H:HEM201 3.1 50.1 1.0
C1D H:HEM201 3.1 50.1 1.0
C4B H:HEM201 3.1 45.2 1.0
C1A H:HEM201 3.1 50.0 1.0
C1B H:HEM201 3.1 46.5 1.0
C4A H:HEM201 3.1 50.1 1.0
C4D H:HEM201 3.1 52.2 1.0
CD2 H:HIS99 3.3 47.3 1.0
CHD H:HEM201 3.4 48.2 1.0
CHC H:HEM201 3.4 47.0 1.0
CHA H:HEM201 3.4 47.9 1.0
CHB H:HEM201 3.5 49.4 1.0
ND1 H:HIS99 4.2 45.3 1.0
CG2 H:VAL71 4.2 49.3 1.0
C3C H:HEM201 4.3 57.8 1.0
C2C H:HEM201 4.3 53.2 1.0
C2A H:HEM201 4.3 51.5 1.0
C3A H:HEM201 4.3 47.8 1.0
C2B H:HEM201 4.3 47.9 1.0
C3B H:HEM201 4.3 51.5 1.0
C2D H:HEM201 4.3 51.8 1.0
C3D H:HEM201 4.3 52.6 1.0
CG H:HIS99 4.4 51.4 1.0
CG1 H:VAL71 4.6 44.5 1.0
CE1 H:HIS67 4.9 52.1 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 05:32:24 2024

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