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Iron in PDB 1f5o: 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)

Protein crystallography data

The structure of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1), PDB code: 1f5o was solved by H.A.Heaslet, W.E.Royer Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 8.00 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 82.500, 96.200, 146.100, 90.00, 90.00, 90.00
R / Rfree (%) 19.2 / 23.4

Iron Binding Sites:

The binding sites of Iron atom in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) (pdb code 1f5o). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 6 binding sites of Iron where determined in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1), PDB code: 1f5o:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6;

Iron binding site 1 out of 6 in 1f5o

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Iron binding site 1 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe150

b:52.5
occ:1.00
FE A:HEM150 0.0 52.5 1.0
NA A:HEM150 2.0 52.5 1.0
ND A:HEM150 2.0 52.5 1.0
NC A:HEM150 2.0 52.5 1.0
NB A:HEM150 2.0 52.5 1.0
NE2 A:HIS105 2.0 33.8 1.0
CE1 A:HIS105 2.9 33.8 1.0
C1A A:HEM150 3.0 52.5 1.0
C1D A:HEM150 3.0 52.5 1.0
C4A A:HEM150 3.0 52.5 1.0
C4C A:HEM150 3.1 52.5 1.0
C4D A:HEM150 3.1 52.5 1.0
C1C A:HEM150 3.1 52.5 1.0
C4B A:HEM150 3.1 52.5 1.0
C1B A:HEM150 3.1 52.5 1.0
CD2 A:HIS105 3.2 33.8 1.0
CHD A:HEM150 3.4 52.5 1.0
CHA A:HEM150 3.4 52.5 1.0
CHB A:HEM150 3.5 52.5 1.0
CHC A:HEM150 3.5 52.5 1.0
ND1 A:HIS105 4.1 33.8 1.0
NE2 A:HIS73 4.2 49.5 1.0
CG A:HIS105 4.3 33.8 1.0
C2D A:HEM150 4.3 52.5 1.0
C2A A:HEM150 4.3 52.5 1.0
C3D A:HEM150 4.3 52.5 1.0
C3A A:HEM150 4.3 52.5 1.0
C2C A:HEM150 4.3 52.5 1.0
C3C A:HEM150 4.3 52.5 1.0
C3B A:HEM150 4.3 52.5 1.0
C2B A:HEM150 4.4 52.5 1.0
CG1 A:ILE77 4.4 37.4 1.0
CD1 A:ILE77 4.4 37.4 1.0

Iron binding site 2 out of 6 in 1f5o

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Iron binding site 2 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe150

b:38.0
occ:1.00
FE B:HEM150 0.0 38.0 1.0
ND B:HEM150 2.0 38.0 1.0
NA B:HEM150 2.0 38.0 1.0
NC B:HEM150 2.0 38.0 1.0
NB B:HEM150 2.0 38.0 1.0
NE2 B:HIS105 2.1 39.2 1.0
CE1 B:HIS105 2.9 39.2 1.0
C1A B:HEM150 3.0 38.0 1.0
C1D B:HEM150 3.0 38.0 1.0
C4D B:HEM150 3.0 38.0 1.0
C4C B:HEM150 3.0 38.0 1.0
C4A B:HEM150 3.1 38.0 1.0
C1C B:HEM150 3.1 38.0 1.0
C4B B:HEM150 3.1 38.0 1.0
C1B B:HEM150 3.1 38.0 1.0
CD2 B:HIS105 3.2 39.2 1.0
CHD B:HEM150 3.4 38.0 1.0
CHA B:HEM150 3.4 38.0 1.0
CHC B:HEM150 3.5 38.0 1.0
CHB B:HEM150 3.5 38.0 1.0
ND1 B:HIS105 4.1 39.2 1.0
NE2 B:HIS73 4.2 39.3 1.0
C2A B:HEM150 4.2 38.0 1.0
C2D B:HEM150 4.3 38.0 1.0
C3D B:HEM150 4.3 38.0 1.0
CG B:HIS105 4.3 39.2 1.0
C3A B:HEM150 4.3 38.0 1.0
C2C B:HEM150 4.3 38.0 1.0
C3C B:HEM150 4.3 38.0 1.0
C3B B:HEM150 4.4 38.0 1.0
C2B B:HEM150 4.4 38.0 1.0
CG1 B:ILE77 4.4 26.0 1.0
CD1 B:ILE77 4.4 26.0 1.0

Iron binding site 3 out of 6 in 1f5o

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Iron binding site 3 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe150

b:42.8
occ:1.00
FE C:HEM150 0.0 42.8 1.0
ND C:HEM150 2.0 42.8 1.0
NC C:HEM150 2.0 42.8 1.0
NA C:HEM150 2.0 42.8 1.0
NB C:HEM150 2.0 42.8 1.0
NE2 C:HIS105 2.1 57.2 1.0
CE1 C:HIS105 3.0 57.2 1.0
C1D C:HEM150 3.0 42.8 1.0
C4D C:HEM150 3.0 42.8 1.0
C4C C:HEM150 3.0 42.8 1.0
C1A C:HEM150 3.0 42.8 1.0
C1C C:HEM150 3.1 42.8 1.0
C4A C:HEM150 3.1 42.8 1.0
C4B C:HEM150 3.1 42.8 1.0
C1B C:HEM150 3.1 42.8 1.0
CD2 C:HIS105 3.2 57.2 1.0
CHD C:HEM150 3.4 42.8 1.0
CHA C:HEM150 3.4 42.8 1.0
CHC C:HEM150 3.5 42.8 1.0
CHB C:HEM150 3.5 42.8 1.0
ND1 C:HIS105 4.2 57.2 1.0
NE2 C:HIS73 4.2 54.7 1.0
C2D C:HEM150 4.3 42.8 1.0
C3D C:HEM150 4.3 42.8 1.0
C2A C:HEM150 4.3 42.8 1.0
CG C:HIS105 4.3 57.2 1.0
C2C C:HEM150 4.3 42.8 1.0
C3C C:HEM150 4.3 42.8 1.0
C3A C:HEM150 4.3 42.8 1.0
C3B C:HEM150 4.3 42.8 1.0
C2B C:HEM150 4.3 42.8 1.0
CG1 C:ILE77 4.4 33.7 1.0
CD1 C:ILE77 4.4 33.7 1.0

Iron binding site 4 out of 6 in 1f5o

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Iron binding site 4 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe150

b:38.2
occ:1.00
FE D:HEM150 0.0 38.2 1.0
ND D:HEM150 2.0 38.2 1.0
NA D:HEM150 2.0 38.2 1.0
NC D:HEM150 2.0 38.2 1.0
NE2 D:HIS105 2.0 53.6 1.0
NB D:HEM150 2.1 38.2 1.0
CE1 D:HIS105 2.9 53.6 1.0
C1D D:HEM150 3.0 38.2 1.0
C4D D:HEM150 3.0 38.2 1.0
C1A D:HEM150 3.0 38.2 1.0
C4A D:HEM150 3.0 38.2 1.0
C4C D:HEM150 3.1 38.2 1.0
C1C D:HEM150 3.1 38.2 1.0
C1B D:HEM150 3.1 38.2 1.0
C4B D:HEM150 3.1 38.2 1.0
CD2 D:HIS105 3.2 53.6 1.0
CHA D:HEM150 3.4 38.2 1.0
CHD D:HEM150 3.4 38.2 1.0
CHB D:HEM150 3.5 38.2 1.0
CHC D:HEM150 3.5 38.2 1.0
ND1 D:HIS105 4.1 53.6 1.0
NE2 D:HIS73 4.2 55.0 1.0
C3D D:HEM150 4.2 38.2 1.0
C2A D:HEM150 4.2 38.2 1.0
C2D D:HEM150 4.2 38.2 1.0
CG D:HIS105 4.3 53.6 1.0
C3A D:HEM150 4.3 38.2 1.0
C2C D:HEM150 4.3 38.2 1.0
C3C D:HEM150 4.3 38.2 1.0
C3B D:HEM150 4.4 38.2 1.0
C2B D:HEM150 4.4 38.2 1.0
CG1 D:ILE77 4.4 30.2 1.0
CD1 D:ILE77 4.4 30.2 1.0

Iron binding site 5 out of 6 in 1f5o

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Iron binding site 5 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe150

b:41.0
occ:1.00
FE E:HEM150 0.0 41.0 1.0
NC E:HEM150 2.0 41.0 1.0
ND E:HEM150 2.0 41.0 1.0
NA E:HEM150 2.0 41.0 1.0
NB E:HEM150 2.0 41.0 1.0
NE2 E:HIS105 2.1 33.8 1.0
CE1 E:HIS105 3.0 33.8 1.0
C1D E:HEM150 3.0 41.0 1.0
C4C E:HEM150 3.0 41.0 1.0
C4D E:HEM150 3.1 41.0 1.0
C1C E:HEM150 3.1 41.0 1.0
C1A E:HEM150 3.1 41.0 1.0
C4B E:HEM150 3.1 41.0 1.0
C4A E:HEM150 3.1 41.0 1.0
C1B E:HEM150 3.1 41.0 1.0
CD2 E:HIS105 3.2 33.8 1.0
CHD E:HEM150 3.4 41.0 1.0
CHC E:HEM150 3.4 41.0 1.0
CHA E:HEM150 3.4 41.0 1.0
CHB E:HEM150 3.5 41.0 1.0
ND1 E:HIS105 4.1 33.8 1.0
NE2 E:HIS73 4.2 58.3 1.0
C2D E:HEM150 4.3 41.0 1.0
C3D E:HEM150 4.3 41.0 1.0
CG E:HIS105 4.3 33.8 1.0
C2C E:HEM150 4.3 41.0 1.0
C2A E:HEM150 4.3 41.0 1.0
C3C E:HEM150 4.3 41.0 1.0
C3A E:HEM150 4.3 41.0 1.0
C3B E:HEM150 4.3 41.0 1.0
C2B E:HEM150 4.3 41.0 1.0
CD1 E:ILE77 4.4 36.2 1.0
CG1 E:ILE77 4.4 36.2 1.0

Iron binding site 6 out of 6 in 1f5o

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Iron binding site 6 out of 6 in the 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of 2.9 Angstrom Crystal Structure of Deoxygenated Lamprey Hemoglobin V in the Space Group P2(1)2(1)2(1) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Fe150

b:42.2
occ:1.00
FE F:HEM150 0.0 42.2 1.0
NA F:HEM150 1.9 42.2 1.0
ND F:HEM150 2.0 42.2 1.0
NB F:HEM150 2.0 42.2 1.0
NC F:HEM150 2.0 42.2 1.0
NE2 F:HIS105 2.1 41.0 1.0
CE1 F:HIS105 2.9 41.0 1.0
C1A F:HEM150 3.0 42.2 1.0
C4A F:HEM150 3.0 42.2 1.0
C4D F:HEM150 3.0 42.2 1.0
C1D F:HEM150 3.1 42.2 1.0
C1B F:HEM150 3.1 42.2 1.0
C4B F:HEM150 3.1 42.2 1.0
C4C F:HEM150 3.1 42.2 1.0
C1C F:HEM150 3.1 42.2 1.0
CD2 F:HIS105 3.2 41.0 1.0
CHA F:HEM150 3.4 42.2 1.0
CHB F:HEM150 3.4 42.2 1.0
CHD F:HEM150 3.5 42.2 1.0
CHC F:HEM150 3.5 42.2 1.0
ND1 F:HIS105 4.2 41.0 1.0
NE2 F:HIS73 4.2 54.6 1.0
C2A F:HEM150 4.2 42.2 1.0
C3A F:HEM150 4.3 42.2 1.0
C3D F:HEM150 4.3 42.2 1.0
C2D F:HEM150 4.3 42.2 1.0
CG F:HIS105 4.3 41.0 1.0
C3B F:HEM150 4.3 42.2 1.0
C2B F:HEM150 4.3 42.2 1.0
C2C F:HEM150 4.3 42.2 1.0
C3C F:HEM150 4.4 42.2 1.0
CG1 F:ILE77 4.4 39.1 1.0
CD1 F:ILE77 4.4 39.1 1.0

Reference:

H.A.Heaslet, W.E.Royer Jr.. Crystalline Ligand Transitions in Lamprey Hemoglobin. Structural Evidence For the Regulation of Oxygen Affinity. J.Biol.Chem. V. 276 26230 2001.
ISSN: ISSN 0021-9258
PubMed: 11340069
DOI: 10.1074/JBC.M101391200
Page generated: Sat Aug 3 04:44:05 2024

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